From 601082705339cc53e071ebc7268c8bdf3d2f44e1 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Mon, 2 May 2022 14:13:31 -0400
Subject: [PATCH 001/110] Updated version to v2.4.8

---
 __version__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/__version__.py b/__version__.py
index a9f7c69a73..b6b2f10e76 100644
--- a/__version__.py
+++ b/__version__.py
@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.7'
+__version__ = '2.4.8'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'

From 17e6bae18051e9c55af8ac89e398543ac48b5643 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 2 May 2022 14:57:37 -0400
Subject: [PATCH 002/110] Added support for all SpatialPy modes.

---
 client/model-view/model-view.js | 32 +++++++++++++++++++++++++-------
 client/model-view/modelView.pug | 15 +++++++++++++--
 2 files changed, 38 insertions(+), 9 deletions(-)

diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js
index ee749e91a9..7267fd628a 100644
--- a/client/model-view/model-view.js
+++ b/client/model-view/model-view.js
@@ -46,6 +46,9 @@ module.exports = View.extend({
     'change [data-hook=all-continuous]' : 'setDefaultMode',
     'change [data-hook=all-discrete]' : 'setDefaultMode',
     'change [data-hook=advanced]' : 'setDefaultMode',
+    'change [data-hook=spatial-continuous]' : 'setDefaultMode',
+    'change [data-hook=spatial-discrete]' : 'setDefaultMode',
+    'change [data-hook=spatial-discrete-concentration]' : 'setDefaultMode',
     'change [data-hook=edit-volume]' : 'updateVolumeViewer',
     'click [data-hook=collapse-mv-advanced-section]' : 'changeCollapseButtonText',
     'click [data-hook=collapse-system-volume]' : 'changeCollapseButtonText'
@@ -76,14 +79,27 @@ module.exports = View.extend({
       this.setReadOnlyMode("model-mode");
       this.setReadOnlyMode("system-volume");
     }else {
-      if(this.model.defaultMode === "" && !this.model.is_spatial){
-        this.getInitialDefaultMode();
+      if(this.model.defaultMode === ""){
+        if(this.model.is_spatial) {
+          this.model.defaultMode = "discrete";
+          $(this.queryByHook("spatial-discrete")).prop('checked', true);
+        }else{
+          this.getInitialDefaultMode();
+        }
       }else {
-        let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'};
-        $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
         if(this.model.is_spatial) {
-          $(this.queryByHook("advanced-model-mode")).css("display", "none");
+          let dataHooks = {
+            'continuous':'spatial-continuous',
+            'discrete':'spatial-discrete',
+            'discrete-concentration':'spatial-discrete-concentration'
+          };
+          $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
+          $(this.queryByHook("model-mode-container")).css("display", "none");
           $(this.queryByHook("system-volume-container")).css("display", "none");
+        }else{
+          let dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'};
+          $(this.queryByHook(dataHooks[this.model.defaultMode])).prop('checked', true);
+          $(this.queryByHook("spatial-model-mode-container")).css("display", "none");
         }
       }
       this.model.reactions.on("change", (reactions) => {
@@ -319,8 +335,10 @@ module.exports = View.extend({
     let prevMode = this.model.defaultMode;
     this.model.defaultMode = e.target.dataset.name;
     this.speciesView.defaultMode = e.target.dataset.name;
-    this.setAllSpeciesModes(prevMode);
-    this.toggleVolumeContainer();
+    if(!this.model.is_spatial) {
+      this.setAllSpeciesModes(prevMode);
+      this.toggleVolumeContainer();
+    }
   },
   setInitialDefaultMode: function (modal, mode) {
     var dataHooks = {'continuous':'all-continuous', 'discrete':'all-discrete', 'dynamic':'advanced'};
diff --git a/client/model-view/modelView.pug b/client/model-view/modelView.pug
index 9284a249c5..def5cf4d6c 100644
--- a/client/model-view/modelView.pug
+++ b/client/model-view/modelView.pug
@@ -32,17 +32,28 @@ div#model-view
           
           hr
 
-          div.row
+          div.row(data-hook="model-mode-container")
             div.col-sm-4
               input.mr-2(type="radio" name="default-mode" data-hook="all-continuous" data-name="continuous")
               span Concentration
             div.col-sm-4
               input.mr-2(type="radio" name="default-mode" data-hook="all-discrete" data-name="discrete")
               span Population
-            div.col-sm-4(data-hook="advanced-model-mode")
+            div.col-sm-4
               input.mr-2(type="radio" name="default-mode" data-hook="advanced" data-name="dynamic")
               span Hybrid Concentration/Population
 
+          div.row(data-hook="spatial-model-mode-container")
+            div.col-sm-4
+              input.mr-2(type="radio" name="default-mode" data-hook="spatial-continuous" data-name="continuous")
+              span Concentration
+            div.col-sm-4
+              input.mr-2(type="radio" name="default-mode" data-hook="spatial-discrete" data-name="discrete")
+              span Population (outpust: absolute value)
+            div.col-sm-4
+              input.mr-2(type="radio" name="default-mode" data-hook="spatial-discrete-concentration" data-name="discrete-concentration")
+              span Population (outputs: scaled by volume)
+
         div.tab-pane(id="view-model-mode" data-hook="view-model-mode")
 
           hr

From 3a1e8a6d43a123e293f6dd1aea94a3ee16e2dff9 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 2 May 2022 14:58:29 -0400
Subject: [PATCH 003/110] Added backward compatability support for spatial
 modes.

---
 stochss/handlers/util/stochss_model.py         | 2 ++
 stochss/handlers/util/stochss_spatial_model.py | 4 ++++
 2 files changed, 6 insertions(+)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index a090934d24..f841d6541c 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -385,6 +385,8 @@ def convert_to_spatial(self):
         if self.model is None:
             model = self.load()
         model['is_spatial'] = True
+        if model['defaultMode'] == "dynamic":
+            model['defaultMode'] == "discrete-concentration"
         if "timestepSize" not in self.model['modelSettings'].keys():
             self.model['modelSettings']['timestepSize'] = 1e-5
         if "domain" not in model.keys():
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index a32a083a4f..c2932c10d6 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -391,6 +391,8 @@ def convert_to_model(self):
         if self.model is None:
             s_model = self.load()
         s_model['is_spatial'] = False
+        if s_model['defaultMode'] == "discrete-concentration":
+            s_model['defaultMode'] == "dynamic"
         if ".wkgp" in self.path:
             wkgp_path = self.get_dir_name()
             wkgp_path, _ = self.get_unique_path(name=self.get_file(path=wkgp_path),
@@ -635,6 +637,8 @@ def load(self):
         self.model['name'] = self.get_name()
         if not self.model['defaultMode']:
             self.model['defaultMode'] = "discrete"
+        elif self.model['defaultMode'] == "dynamic":
+            self.model['defaultMode'] = "discrete-concentration"
         if "timestepSize" not in self.model['modelSettings'].keys():
             self.model['modelSettings']['timestepSize'] = 1e-5
         self.__update_domain()

From 40d571f396992e30ddf462585d7016ba952e488e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 2 May 2022 15:16:41 -0400
Subject: [PATCH 004/110] Fixed spelling error.  Only log errors if they exist.

---
 stochss/handlers/file_browser.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/file_browser.py b/stochss/handlers/file_browser.py
index 7bccf87585..0dde9679a6 100644
--- a/stochss/handlers/file_browser.py
+++ b/stochss/handlers/file_browser.py
@@ -709,7 +709,8 @@ async def get(self):
             log.debug(f"Exec command: {exec_cmd}")
             pipe = subprocess.Popen(exec_cmd, stdout=subprocess.PIPE, text=True)
             results, error = pipe.communicate()
-            log.error(f"Errors trown by the subprocess: {error}")
+            if error is not None:
+                log.error(f"Errors thrown by the subprocess: {error}")
             resp = json.loads(results)
             log.debug(f"Response: {resp}")
             self.write(resp)

From 8fe94483e65efe13b5172b7bc1e4fc9ec4e49fad Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:05:59 -0400
Subject: [PATCH 005/110] Added support for new ode propensity functions.

---
 stochss/handlers/util/stochss_model.py         | 7 ++++++-
 stochss/handlers/util/stochss_spatial_model.py | 5 +++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index a090934d24..0bbe55baa4 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -165,15 +165,18 @@ def __convert_reactions(self, model):
                 if reaction['reactionType'] == "custom-propensity":
                     rate = None
                     propensity = reaction['propensity']
+                    ode_propensity = reaction['odePropensity']
                 else:
                     rate = g_parameters[reaction['rate']['name']]
                     propensity = None
+                    ode_propensity = None
                 reactants, products = self.__convert_stoich_species(reaction=reaction)
                 g_reaction = Reaction(name=reaction['name'],
                                       reactants=reactants,
                                       products=products,
                                       rate=rate,
-                                      propensity_function=propensity)
+                                      propensity_function=propensity,
+                                      ode_propensity_function=ode_propensity)
                 model.add_reaction(g_reaction)
         except KeyError as err:
             message = "Reactions are not properly formatted or "
@@ -295,6 +298,8 @@ def __update_reactions(self):
         if "reactions" not in self.model.keys():
             return
         for reaction in self.model['reactions']:
+            if "odePropensity" not in reaction.keys():
+                reaction['odePropensity'] = reaction['propensity']
             try:
                 if reaction['rate'].keys() and isinstance(reaction['rate']['expression'], str):
                     expression = ast.literal_eval(reaction['rate']['expression'])
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index a32a083a4f..4b9b0cf513 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -246,9 +246,11 @@ def __convert_reactions(self, model, type_ids):
                 if reaction['reactionType'] != "custom-propensity":
                     rate = s_params[reaction['rate']['name']]
                     propensity = None
+                    ode_propensity = None
                 else:
                     rate = None
                     propensity = reaction['propensity']
+                    ode_propensity = reaction['odePropensity']
                 types = [type_ids[d_type] for d_type in reaction['types']]
                 if len(types) == len(type_ids):
                     types = None
@@ -257,6 +259,7 @@ def __convert_reactions(self, model, type_ids):
                                       products=products,
                                       rate=rate,
                                       propensity_function=propensity,
+                                      ode_propensity_function=ode_propensity,
                                       restrict_to=types)
                 model.add_reaction(s_reaction)
         except KeyError as err:
@@ -647,6 +650,8 @@ def load(self):
                 diff = 0.0 if "diffusionCoeff" not in species.keys() else species['diffusionCoeff']
                 species['diffusionConst'] = diff
         for reaction in self.model['reactions']:
+            if "odePropensity" not in reaction.keys():
+                reaction['odePropensity'] = reaction['propensity']
             if "types" not in reaction.keys():
                 reaction['types'] = list(range(1, len(self.model['domain']['types'])))
         return self.model

From 7161ced0b9d9b82b93e27983a47d29e150cd1085 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:16:11 -0400
Subject: [PATCH 006/110] Fixed updateReactionType function.  Added function to
 build massaction propensities.  Added ode propensity support.

---
 client/models/reaction.js | 59 +++++++++++++++++++++++++++++----------
 1 file changed, 45 insertions(+), 14 deletions(-)

diff --git a/client/models/reaction.js b/client/models/reaction.js
index 3edcbe8941..262103d508 100644
--- a/client/models/reaction.js
+++ b/client/models/reaction.js
@@ -27,9 +27,8 @@ module.exports = State.extend({
   props: {
     compID: 'number',
     name: 'string',
-    reactionType: 'string',
-    summary: 'string',
     massaction: 'boolean',
+    odePropensity: 'string',
     propensity: 'string',
     annotation: 'string',
     types: 'object'
@@ -42,29 +41,58 @@ module.exports = State.extend({
     products: StoichSpecies
   },
   session: {
-    selected: {
+    hasConflict: {
       type: 'boolean',
-      default: true,
+      default: false,
     },
-    hasConflict: {
+    maODEPropensity: 'string',
+    maPropensity: 'string',
+    mirrorPropensities: 'boolean',
+    reactionType: 'string',
+    selected: {
       type: 'boolean',
       default: false,
     },
+    summary: 'string'
   },
   initialize: function (attrs, options) {
     var self = this;
     State.prototype.initialize.apply(this, arguments);
-    if(!this.reactionType.startsWith('custom')) {
-      let reactionType = this.updateReactionType();
-      if(this.reactionType !== reactionType){
-        this.reactionType = reactionType
-        this.buildSummary()
+    this.reactionType = this.updateReactionType();
+    this.mirrorPropensities = this.propensity === this.odePropensity;
+    this.buildSummary();
+    this.buildMAPropensities();
+    this.checkModes();
+    this.on('change-reaction', () => {
+      this.buildSummary();
+      this.buildMAPropensities();
+      this.checkModes();
+    });
+  },
+  buildMAPropensities: function () {
+    if(this.reactionType === "custom-propensity") { return }
+    var odePropensity = this.rate.name;
+    var propensity = this.rate.name;
+    
+    this.reactants.forEach((stoichSpecies) => {
+      let name = stoichSpecies.specie.name;
+      if(stoichSpecies.ratio == 2) {
+        odePropensity += ` * ${name} * ${name}`;
+        propensity = `0.5 * ${propensity} * ${name} * (${name} - 1) / vol`;
+      }else{
+        odePropensity += ` * ${name}`;
+        propensity += ` * ${name}`;
       }
+    })
+    
+    let order = this.reactants.length;
+    if(order == 2) {
+      propensity += " / vol";
+    }else if(order == 0) {
+      propensity += " * vol"
     }
-    this.on('change-reaction', function () {
-      self.buildSummary();
-      self.checkModes();
-    });
+    this.maODEPropensity = odePropensity;
+    this.maPropensity = propensity;
   },
   buildSummary: function () {
     var summary = "";
@@ -137,6 +165,9 @@ module.exports = State.extend({
     this.hasConflict = Boolean(hasContinuous && (hasDynamic || hasDiscrete))
   },
   updateReactionType: function () {
+    if(!this.massaction) {
+      return "custom-propensity"
+    }
     let numReactants = this.reactants.length
     let numProducts = this.products.length
     let prodRatio1 = numProducts > 0 ? this.products.models[0].ratio : 0

From ff9c1c43af1bab14083fb9501162cbd4c3a07b99 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:18:43 -0400
Subject: [PATCH 007/110] Added ode propensity and massaction propensity
 support.  Refactored getDefaultSpecies to use as many unique species as
 possible when creating reactants and products.

---
 client/models/reactions.js | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/client/models/reactions.js b/client/models/reactions.js
index eb4e1d6861..f609f339c5 100644
--- a/client/models/reactions.js
+++ b/client/models/reactions.js
@@ -31,13 +31,13 @@ Reactions = Collection.extend({
   addReaction: function (reactionType, stoichArgs, types) {
     var id = this.parent.getDefaultID();
     var name = this.getDefaultName();
-    var massaction = reactionType === 'custom-massaction';
+    var massaction = reactionType !== 'custom-propensity';
     var reaction = new Reaction({
       compID: id,
       name: name,
-      reactionType: reactionType,
       massaction: massaction,
       propensity: '',
+      odePropensity: '',
       annotation: '',
       types: types,
       reactants: stoichArgs.reactants,
@@ -47,9 +47,12 @@ Reactions = Collection.extend({
     this.setDefaultSpecieForStoichSpecies(reaction.products);
     if(reactionType !== 'custom-propensity')
       reaction.rate = this.getDefaultRate();
-    reaction.buildSummary()
+    reaction.buildSummary();
+    reaction.buildMAPropensities();
+    reaction.reactionType = reactionType;
+    reaction.selected = true;
     this.add(reaction);
-    this.parent.updateValid()
+    this.parent.updateValid();
     return reaction;
   },
   getDefaultName: function () {
@@ -64,11 +67,14 @@ Reactions = Collection.extend({
   },
   setDefaultSpecieForStoichSpecies: function (stoichSpecies) {
     stoichSpecies.forEach(function (stoichSpecie) {
-      stoichSpecie.specie = this.getDefaultSpecie();
+      stoichSpecie.specie = this.getDefaultSpecie(stoichSpecies.indexOf(stoichSpecie));
     }, this);
   },
-  getDefaultSpecie: function () {
-    var specie = this.parent.species.at(0);
+  getDefaultSpecie: function (index) {
+    if(this.parent.species.length <= index) {
+      index -= this.parent.species.length;
+    }
+    var specie = this.parent.species.at(index);
     return specie;
   },
   getDefaultRate: function () {

From 3ba02110eff2986e871dbe449190cec531b50b0b Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:21:28 -0400
Subject: [PATCH 008/110] Added support for Collection.get using compID as the
 key.

---
 client/models/parameters.js | 1 +
 client/models/species.js    | 1 +
 2 files changed, 2 insertions(+)

diff --git a/client/models/parameters.js b/client/models/parameters.js
index 520418a72d..2279bc59ee 100644
--- a/client/models/parameters.js
+++ b/client/models/parameters.js
@@ -24,6 +24,7 @@ var Collection = require('ampersand-collection');
 
 module.exports = Collection.extend({
   model: Parameter,
+  indexes: ['compID'],
   addParameter: function () {
     var id = this.parent.getDefaultID();
     var name = this.getDefaultName();
diff --git a/client/models/species.js b/client/models/species.js
index 2e822cfc5b..dcba8eadc2 100644
--- a/client/models/species.js
+++ b/client/models/species.js
@@ -24,6 +24,7 @@ var Collection = require('ampersand-collection');
 
 module.exports = Collection.extend({
   model: Specie,
+  indexes: ['compID'],
   addSpecie: function (types) {
     var id = this.parent.getDefaultID();
     var name = this.getDefaultName();

From 02ca9571abd9dfcdda5f74359cb78cc8b50c9768 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:22:58 -0400
Subject: [PATCH 009/110] Added optional arg for ratio when adding new
 reactants or products.

---
 client/models/stoich-species.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/models/stoich-species.js b/client/models/stoich-species.js
index 70cff4ecb5..4fc9006f68 100644
--- a/client/models/stoich-species.js
+++ b/client/models/stoich-species.js
@@ -32,12 +32,12 @@ module.exports = Collection.extend({
     this.baseModel = this.parent.collection.parent;
     this.baseModel.species.trigger('stoich-species-change');
   },
-  addStoichSpecie: function (specieName) {
+  addStoichSpecie: function (specieName, {ratio=1}={}) {
     var specie = this.parent.collection.parent.species.filter(function (specie) {
         return specie.name === specieName;
     })[0];
     var stoichSpecie = new StoichSpecie({
-        ratio: 1
+        ratio: ratio
     });
     stoichSpecie.specie = specie;
     this.add(stoichSpecie);

From 24ffd589bb268ba5739d4dd138facfbe792d1f1f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:24:04 -0400
Subject: [PATCH 010/110] Added support for a disabled attribute.

---
 client/views/input.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/views/input.js b/client/views/input.js
index e4531e0732..3e2ba786cc 100644
--- a/client/views/input.js
+++ b/client/views/input.js
@@ -24,6 +24,7 @@ module.exports = AmpersandInputView.extend({
     label: 'string',
     modelKey: 'string',
     valueType: 'string',
+    disabled: 'boolean'
   },
   events: {
     'input input' : 'changeInputHandler',
@@ -32,11 +33,12 @@ module.exports = AmpersandInputView.extend({
     AmpersandInputView.prototype.initialize.apply(this, arguments);
   },
   render: function () {
+    let disabled = this.disabled ? "disabled" : "";
     if(this.label) {
       this.template = [
         '<label>',
             '<span data-hook="label"></span>',
-            '<input class="form-input labeled">',
+            `<input class="form-input labeled" ${disabled}>`,
             '<div data-hook="message-container" class="message message-below message-error text-danger">',
                 '<p data-hook="message-text"></p>',
             '</div>',
@@ -45,7 +47,7 @@ module.exports = AmpersandInputView.extend({
     }else{
       this.template = [
         '<label>',
-            '<input class="form-input">',
+            `<input class="form-input" ${disabled}>`,
             '<div data-hook="message-container" class="message message-below message-error text-danger">',
                 '<p data-hook="message-text"></p>',
             '</div>',

From b44eccee63e5bf9fd036a7528e357212787febea Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:24:47 -0400
Subject: [PATCH 011/110] Added tooltip for ODE Propensity functions.

---
 client/tooltips.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/client/tooltips.js b/client/tooltips.js
index 1049db9302..f813076494 100644
--- a/client/tooltips.js
+++ b/client/tooltips.js
@@ -53,6 +53,8 @@ module.exports = {
     rate: "The rate of the mass-action reaction.",
     
     propensity: "The custom propensity expression for the reaction.",
+
+    odePropensity: "The custom ode propensity expression for the reaction.",
     
     reactant: "The reactants that are consumed in the reaction, with stoichiometry.",
     

From da9fa771413b8403aad771c1ecaa1afbd332ad49 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:26:20 -0400
Subject: [PATCH 012/110] updated the labels for custom reaction types to use
 title case.

---
 client/reaction-types.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/reaction-types.js b/client/reaction-types.js
index 4ff9516b32..f8a2e3f8e4 100644
--- a/client/reaction-types.js
+++ b/client/reaction-types.js
@@ -55,11 +55,11 @@ module.exports = {
   'custom-massaction': {
     reactants: [ { ratio: 1 } ],
     products: [ { ratio: 1 } ],
-    label: 'Custom mass action'
+    label: 'Custom Mass Action'
   },
   'custom-propensity': {
     reactants: [ { ratio: 1 } ],
     products: [ { ratio: 1 } ],
-    label: 'Custom propensity'
+    label: 'Custom Propensity'
   }
 }

From 96e792600b7ebc5e233da2183e9a8900ac245bd8 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:29:11 -0400
Subject: [PATCH 013/110] Added support for reaction type labels to display
 when disabled.  Updates to existing class css rules.

---
 client/styles/styles.css | 32 +++++++++++++++++++++++++++-----
 1 file changed, 27 insertions(+), 5 deletions(-)

diff --git a/client/styles/styles.css b/client/styles/styles.css
index e5c6744d2d..6ddb695ddc 100644
--- a/client/styles/styles.css
+++ b/client/styles/styles.css
@@ -130,8 +130,8 @@ label {
 }
 
 span.custom {
-  padding-right: 0.25rem;
-  padding-left: 0.25rem;
+  padding-right: 0.5rem;
+  padding-left: 0.5rem;
 }
 
 button.custom {
@@ -302,7 +302,6 @@ input[type="file"]::-ms-browse {
 
 .reaction-list-summary {
   width: auto !important;
-  text-align: center;
 }
 
 .container-part {
@@ -649,13 +648,32 @@ span.checkbox {
   height: auto;
 }
 
+.dropdown-item.rtype.disabled {
+  pointer-events: auto !important;
+}
+
 .reaction-lb2 {
   display: none;
 }
 
-.dropdown-item:hover .reaction-lb2 {
+.dropdown-item:not(.disabled):hover .reaction-lb2 {
   position: absolute;
-  left: 195px;
+  left: 196px;
+  display: inline-block;
+  background-color: black;
+  color: white;
+  box-shadow: 0px 8px 16px 0px rgba(0,0,0,0.2);
+  border: .5px solid rgb(228, 229, 230) !important;
+  padding: 0px 5px;
+}
+
+.reaction-lb3 {
+  display: none;
+}
+
+.dropdown-item.disabled:hover .reaction-lb3 {
+  position: absolute;
+  left: 196px;
   display: inline-block;
   background-color: black;
   color: white;
@@ -727,3 +745,7 @@ span.checkbox {
   margin-top: 64px;
   padding: 20px 16px;
 }
+
+.hidden {
+  display: none;
+}

From 7cf24943e83941569220c1cb358fcc9af47326f4 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:32:14 -0400
Subject: [PATCH 014/110] Renamed the reaction domain types files to reaction
 restrict to.  Minor updates.

---
 ...{reactionTypes.pug => reactionRestrictTo.pug} |  0
 ...reaction-types.js => reaction-restrict-to.js} | 16 ++++++++--------
 2 files changed, 8 insertions(+), 8 deletions(-)
 rename client/model-view/templates/{reactionTypes.pug => reactionRestrictTo.pug} (100%)
 rename client/model-view/views/{reaction-types.js => reaction-restrict-to.js} (79%)

diff --git a/client/model-view/templates/reactionTypes.pug b/client/model-view/templates/reactionRestrictTo.pug
similarity index 100%
rename from client/model-view/templates/reactionTypes.pug
rename to client/model-view/templates/reactionRestrictTo.pug
diff --git a/client/model-view/views/reaction-types.js b/client/model-view/views/reaction-restrict-to.js
similarity index 79%
rename from client/model-view/views/reaction-types.js
rename to client/model-view/views/reaction-restrict-to.js
index 6cf01751e9..7f48966fc8 100644
--- a/client/model-view/views/reaction-types.js
+++ b/client/model-view/views/reaction-restrict-to.js
@@ -18,9 +18,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 //views
 let View = require('ampersand-view');
-let TypesView = require('./component-types');
+let DomainTypesView = require('./component-types');
 //templates
-let template = require('../templates/reactionTypes.pug');
+let template = require('../templates/reactionRestrictTo.pug');
 
 module.exports = View.extend({
   template: template,
@@ -31,15 +31,15 @@ module.exports = View.extend({
   },
   render: function () {
     View.prototype.render.apply(this, arguments);
-    this.renderTypes();
+    this.renderDomainTypes();
   },
-  renderTypes: function () {
-    if(this.typesView) {
-      this.typesView.remove();
+  renderDomainTypes: function () {
+    if(this.domainTypesView) {
+      this.domainTypesView.remove();
     }
-    this.typesView = this.renderCollection(
+    this.domainTypesView = this.renderCollection(
       this.baseModel.domain.types,
-      TypesView,
+      DomainTypesView,
       this.queryByHook("reaction-types-container"),
       {"filter": function (model) {
         return model.typeID != 0;

From 117ab90260b1bdcedc5e290f03a19be5c08717e2 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:35:47 -0400
Subject: [PATCH 015/110] Combine the standard stoich species view with the
 custom stoich species view.  Reafactored to support new reaction view.

---
 .../templates/editCustomStoichSpecie.pug      |  10 --
 .../model-view/templates/editStoichSpecie.pug |   6 -
 .../model-view/templates/stoichSpecieView.pug |  21 +++
 client/model-view/views/edit-stoich-specie.js |  62 --------
 ...toich-specie.js => stoich-species-view.js} | 148 ++++++++++--------
 5 files changed, 106 insertions(+), 141 deletions(-)
 delete mode 100644 client/model-view/templates/editCustomStoichSpecie.pug
 delete mode 100644 client/model-view/templates/editStoichSpecie.pug
 create mode 100644 client/model-view/templates/stoichSpecieView.pug
 delete mode 100644 client/model-view/views/edit-stoich-specie.js
 rename client/model-view/views/{edit-custom-stoich-specie.js => stoich-species-view.js} (51%)

diff --git a/client/model-view/templates/editCustomStoichSpecie.pug b/client/model-view/templates/editCustomStoichSpecie.pug
deleted file mode 100644
index 5f0d1a6d7f..0000000000
--- a/client/model-view/templates/editCustomStoichSpecie.pug
+++ /dev/null
@@ -1,10 +0,0 @@
-div
-  div.inline
-    button.btn.btn-outline-secondary(class='btn-sm', data-hook='decrement') -
-  span.custom(data-hook="ratio")
-  div.inline
-    button.btn.btn-outline-secondary(class='btn-sm', data-hook='increment') +
-  select(data-hook="select-stoich-specie")
-    span.message.message-below.message-error(data-hook="message-container")
-      p(data-hook="message-text")
-  button.btn.btn-outline-secondary.custom(class='btn-sm', data-hook='remove') X
\ No newline at end of file
diff --git a/client/model-view/templates/editStoichSpecie.pug b/client/model-view/templates/editStoichSpecie.pug
deleted file mode 100644
index 34e754e846..0000000000
--- a/client/model-view/templates/editStoichSpecie.pug
+++ /dev/null
@@ -1,6 +0,0 @@
-div
-  label.select
-    span(data-hook="ratio")
-    select(data-hook="select-stoich-specie")
-      span.message.message-below.message-error(data-hook="message-container")
-        p(data-hook="message-text")
\ No newline at end of file
diff --git a/client/model-view/templates/stoichSpecieView.pug b/client/model-view/templates/stoichSpecieView.pug
new file mode 100644
index 0000000000..073d00ec0b
--- /dev/null
+++ b/client/model-view/templates/stoichSpecieView.pug
@@ -0,0 +1,21 @@
+div
+
+  label.select
+
+    div.inline(data-hook="custom-decrement")
+
+      button.btn.btn-outline-secondary.btn-sm(data-hook='decrement') -
+
+    span.custom(data-hook="ratio")
+
+    div.inline(data-hook="custom-increment")
+    
+      button.btn.btn-outline-secondary.btn-sm(data-hook='increment') +
+
+    select(data-hook="select-stoich-specie")
+
+      span.message.message-below.message-error(data-hook="message-container")
+
+        p(data-hook="message-text")
+
+    button.btn.btn-outline-secondary.custom.btn-sm(data-hook='custom-remove') X
diff --git a/client/model-view/views/edit-stoich-specie.js b/client/model-view/views/edit-stoich-specie.js
deleted file mode 100644
index e4d15bdc24..0000000000
--- a/client/model-view/views/edit-stoich-specie.js
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-var $ = require('jquery');
-//views
-var SelectView = require('ampersand-select-view');
-//templates
-var template = require('../templates/editStoichSpecie.pug');
-
-module.exports = SelectView.extend({
-  // SelectView expects a string template, so pre-render it
-  template: template(),
-  bindings: {
-    'model.ratio' : {
-      hook: 'ratio'
-    }
-  },
-  events: {
-    'change select' : 'selectChangeHandler'
-  },
-  initialize: function () {
-    SelectView.prototype.initialize.apply(this, arguments);
-    this.value = this.model.specie || null;
-  },
-  render: function() {
-    SelectView.prototype.render.apply(this, arguments);
-  },
-  update: function () {
-  },
-  selectChangeHandler: function (e) {
-    var species = this.getSpeciesCollection();
-    var reactions = this.getReactionsCollection();
-    var specie = species.filter(function (m) {
-      return m.name === e.target.selectedOptions.item(0).text;
-    })[0];
-    this.model.specie = specie;
-    this.value = specie;
-    reactions.trigger("change");
-    this.model.collection.parent.trigger('change-reaction')
-  },
-  getReactionsCollection: function () {
-    return this.model.collection.parent.collection;
-  },
-  getSpeciesCollection: function () {
-    return this.model.collection.parent.collection.parent.species;
-  },
-});
\ No newline at end of file
diff --git a/client/model-view/views/edit-custom-stoich-specie.js b/client/model-view/views/stoich-species-view.js
similarity index 51%
rename from client/model-view/views/edit-custom-stoich-specie.js
rename to client/model-view/views/stoich-species-view.js
index dbab386e20..01df300036 100644
--- a/client/model-view/views/edit-custom-stoich-specie.js
+++ b/client/model-view/views/stoich-species-view.js
@@ -16,14 +16,13 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-var $ = require('jquery');
+let $ = require('jquery');
 //views
-var SelectView = require('ampersand-select-view');
+let SelectView = require('ampersand-select-view');
 //templates
-var template = require('../templates/editCustomStoichSpecie.pug');
+let template = require('../templates/stoichSpecieView.pug');
 
 module.exports = SelectView.extend({
-  // SelectView expects a string template, so pre-render it
   template: template(),
   bindings: {
     'model.ratio' : {
@@ -32,47 +31,82 @@ module.exports = SelectView.extend({
   },
   events: {
     'change select' : 'selectChangeHandler',
-    'click [data-hook=increment]' : 'handleIncrement',
     'click [data-hook=decrement]' : 'handleDecrement',
-    'click [data-hook=remove]' : 'deleteSpecie'
+    'click [data-hook=increment]' : 'handleIncrement',
+    'click [data-hook=custom-remove]' : 'deleteSpecie'
   },
-  initialize: function (args) {
-    var self = this;
+  initialize: function () {
     SelectView.prototype.initialize.apply(this, arguments);
-    this.value = this.model.specie || null;
-    this.isReactants = this.parent.parent.isReactants;
-    this.reactionType = this.parent.parent.reactionType;
-    this.stoichSpecies = this.parent.parent.collection;
-    this.stoichSpecies.on('add', function () {
-      self.toggleIncrementButton();
-    });
-    this.stoichSpecies.on('remove', function () {
-      self.toggleIncrementButton();
+    this.value = this.model.specie.compID;
+    if(this.parent.parent.custom) {
+      this.isReactants = this.parent.parent.isReactants;
+      this.reactionType = this.parent.parent.reactionType;
+      this.stoichSpecies = this.parent.parent.collection;
+      this.stoichSpecies.on('add', () => {
+        this.toggleIncrementButton();
+      });
+      this.stoichSpecies.on('remove', () => {
+        this.toggleIncrementButton();
+      });
+    }
+  },
+  render: function() {
+    SelectView.prototype.render.apply(this, arguments);
+    if(this.parent.parent.custom) {
+      this.toggleDecrementButton();
+      this.toggleIncrementButton();
+    }else{
+      $(this.queryByHook('custom-decrement')).css('display', 'none');
+      $(this.queryByHook('custom-increment')).css('display', 'none');
+      $(this.queryByHook('custom-remove')).css('display', 'none');
+    }
+    this.model.collection.parent.on('change-reaction', () => {
+      var setValueFirstModel = () => {
+        if(!this.options.length) {
+          return;
+        }
+        if(this.yieldModel) {
+          this.setValue(this.options.models[0]);
+        }
+        else {
+          this.setValue(this.options.models[0][this.idAttribute]);
+        }
+      };
+
+      this.renderOptions();
+      if (this.hasOptionByValue(this.value)) {
+        this.updateSelectedOption();
+      }
+      else {
+        setValueFirstModel();
+      }
     });
   },
-  render: function () {
-    SelectView.prototype.render.apply(this);
-    this.toggleIncrementButton();
-    this.toggleDecrementButton();
+  deleteSpecie: function () {
+    if(!this.model.collection.parent.reactionType.startsWith('custom')) { return }
+    let reaction = this.model.collection.parent;
+    this.collection.removeStoichSpecie(this.model);
+    reaction.trigger('change-reaction');
+    this.parent.parent.toggleAddSpecieButton();
   },
-  selectChangeHandler: function (e) {
-    var species = this.getSpeciesCollection();
-    var reactions = this.getReactionsCollection();
-    var specie = species.filter(function (m) {
-      return m.name === e.target.selectedOptions.item(0).text;
-    })[0];
-    this.model.specie = specie;
-    this.value = specie;
-    reactions.trigger("change");
-    this.model.collection.parent.trigger('change-reaction')
+  getReactionsCollection: function () {
+    return this.model.collection.parent.collection;
   },
   getSpeciesCollection: function () {
     return this.model.collection.parent.collection.parent.species;
   },
-  getReactionsCollection: function () {
-    return this.model.collection.parent.collection;
+  handleDecrement: function () {
+    if(!this.model.collection.parent.reactionType.startsWith('custom')) { return }
+    this.model.ratio--;
+    this.model.collection.parent.trigger('change-reaction')
+    this.toggleDecrementButton();
+    if(this.validateRatioIncrement()){
+      this.toggleIncrementButton();
+      this.parent.parent.toggleAddSpecieButton();
+    }
   },
   handleIncrement: function () {
+    if(!this.model.collection.parent.reactionType.startsWith('custom')) { return }
     if(this.validateRatioIncrement()){
       this.model.ratio++;
       this.toggleIncrementButton();
@@ -81,41 +115,29 @@ module.exports = SelectView.extend({
     }
     this.toggleDecrementButton();
   },
+  selectChangeHandler: function (e) {
+    let species = this.getSpeciesCollection();
+    let reactions = this.getReactionsCollection();
+    let specie = species.get(e.target.selectedOptions.item(0).value, 'compID');
+    this.model.specie = specie;
+    this.value = specie.compID;
+    reactions.trigger("change");
+    this.model.collection.parent.trigger('change-reaction')
+  },
+  toggleDecrementButton: function () {
+    $(this.queryByHook('decrement')).prop('disabled', this.model.ratio <= 1);
+  },
+  toggleIncrementButton: function () {
+    $(this.queryByHook('increment')).prop('disabled', !this.validateRatioIncrement());
+  },
+  update: function () {},
   validateRatioIncrement: function () {
     if(this.stoichSpecies.length < 2 && this.model.ratio < 2)
       return true;
-    if(this.reactionType !== 'custom-massaction')
+    if(this.reactionType === 'custom-propensity')
       return true;
     if(!this.isReactants)
       return true;
     return false;
-  },
-  toggleIncrementButton: function () {
-    if(!this.validateRatioIncrement()){
-      $(this.queryByHook('increment')).prop('disabled', true);
-    }else{
-      $(this.queryByHook('increment')).prop('disabled', false);
-    }
-  },
-  toggleDecrementButton: function () {
-    if(this.model.ratio <= 1)
-      $(this.queryByHook('decrement')).prop('disabled', true);
-    else
-      $(this.queryByHook('decrement')).prop('disabled', false);
-  },
-  handleDecrement: function () {
-    this.model.ratio--;
-    this.model.collection.parent.trigger('change-reaction')
-    this.toggleDecrementButton();
-    if(this.validateRatioIncrement()){
-      this.toggleIncrementButton();
-      this.parent.parent.toggleAddSpecieButton();
-    }
-  },
-  deleteSpecie: function () {
-    var reaction = this.model.collection.parent
-    this.collection.removeStoichSpecie(this.model);
-    reaction.trigger('change-reaction')
-    this.parent.parent.toggleAddSpecieButton();
-  },
+  }
 });
\ No newline at end of file

From 1ffa421b7a840ab1b24172d2f7d610c2cdf0d789 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:36:58 -0400
Subject: [PATCH 016/110] Added support for ODE Propensity functions.

---
 client/model-view/templates/viewReaction.pug | 28 ++++++++++++++++----
 1 file changed, 23 insertions(+), 5 deletions(-)

diff --git a/client/model-view/templates/viewReaction.pug b/client/model-view/templates/viewReaction.pug
index 21be6b3275..6c45bdc68a 100644
--- a/client/model-view/templates/viewReaction.pug
+++ b/client/model-view/templates/viewReaction.pug
@@ -5,20 +5,38 @@ div.mx-1
 
   div.row.align-items-baseline
 
-    div.col-md-2
+    div.col-sm-2
 
       div.pl-2=this.model.name
 
-    div.col-md-3(data-hook="summary")
+    div.col-sm-3(data-hook="summary")    
 
-    div.col-md-3=this.rate
+    if this.model.massaction
+      div.col-sm-3
+        
+        div=this.rate
+    else
+      div.col-sm-3
 
+        h5 
+
+          span Stochastic Propensity Function:
+
+        div.pl-3=this.model.propensity
+        
+        if !this.model.mirrorPropensities
+          h5 
+
+            span ODE Propensity Function:
+          
+          div.pl-3=this.model.odePropensity
+    
     if this.model.collection.parent.is_spatial
-      div.col-md-2(data-hook="reaction-types")
+      div.col-sm-2(data-hook="reaction-types")
 
         div=this.types.join(', ')
     
-    div.col-md-2(data-hook="reaction-annotation-header")
+    div.col-sm-2(data-hook="reaction-annotation-header")
 
       if this.model.annotation
         div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation) <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="file-alt" class="svg-inline--fa fa-file-alt fa-w-12" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><path fill="currentColor" d="M224 136V0H24C10.7 0 0 10.7 0 24v464c0 13.3 10.7 24 24 24h336c13.3 0 24-10.7 24-24V160H248c-13.2 0-24-10.8-24-24zm64 236c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-64c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-72v8c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm96-114.1v6.1H256V0h6.1c6.4 0 12.5 2.5 17 7l97.9 98c4.5 4.5 7 10.6 7 16.9z"></path></svg>

From 6665f109098c3cc41218de16104c54af1f6a62b3 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:39:59 -0400
Subject: [PATCH 017/110] Refactored to support the new stoich species view and
 reaction view.

---
 .../model-view/templates/reactantProduct.pug  |  13 +-
 client/model-view/views/reactant-product.js   | 112 ++++++++++--------
 2 files changed, 68 insertions(+), 57 deletions(-)

diff --git a/client/model-view/templates/reactantProduct.pug b/client/model-view/templates/reactantProduct.pug
index 72578cf9f3..65d07ac51d 100644
--- a/client/model-view/templates/reactantProduct.pug
+++ b/client/model-view/templates/reactantProduct.pug
@@ -6,9 +6,12 @@ div(data-hook="reaction-details")
 
       div.tooltip-icon(data-hook="field-title-tooltip" data-html="true" data-toggle="tooltip" title="") <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
-  div(data-hook="reactants-editor")
+  div(data-hook=this.hookAnchor + "-editor")
 
-  div(data-hook="collapse", class="collapse")
-    div.row(data-hook="add-specie-container")
-      div(data-hook="select-specie")
-      button.btn.btn-outline-secondary(class="btn-sm", data-hook="add-selected-specie") add
\ No newline at end of file
+  div.hidden(data-hook="custom-" + this.hookAnchor)
+    
+    div.row(data-hook=this.hookAnchor + "-add-specie-container")
+    
+      div(data-hook=this.hookAnchor + "-select-specie")
+    
+      button.btn.btn-outline-secondary(class="btn-sm", data-hook=this.hookAnchor + "-add-selected-specie") add
diff --git a/client/model-view/views/reactant-product.js b/client/model-view/views/reactant-product.js
index d10f54923a..f3b82d54b9 100644
--- a/client/model-view/views/reactant-product.js
+++ b/client/model-view/views/reactant-product.js
@@ -17,68 +17,96 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
 let $ = require('jquery');
-//models
-let StoichSpecie = require('../../models/stoich-specie');
+//support files
+let app = require('../../app');
 //views
 let View = require('ampersand-view');
 let SelectView = require('ampersand-select-view');
-let EditStoichSpecieView = require('./edit-stoich-specie');
-let EditCustomStoichSpecieView = require('./edit-custom-stoich-specie');
+let StoichSpeciesView = require('./stoich-species-view');
 //templates
 let template = require('../templates/reactantProduct.pug');
 
 module.exports = View.extend({
   template: template,
-  events: {
-    'change [data-hook=select-specie]' : 'selectSpecie',
-    'click [data-hook=add-selected-specie]' : 'addSelectedSpecie'
+  events: function () {
+    let events = {};
+    events[`change [data-hook=${this.hookAnchor}-select-specie]`] = 'selectSpecie';
+    events[`click [data-hook=${this.hookAnchor}-add-selected-specie]`] = 'addSelectedSpecie';
+    return events;
   },
   initialize: function (args) {
     View.prototype.initialize.apply(this, arguments);
     this.collection = args.collection;
     this.species = args.species;
     this.reactionType = args.reactionType;
-    this.isReactants = args.isReactants
+    this.custom = args.reactionType.startsWith('custom');
+    this.isReactants = args.isReactants;
     this.unselectedText = 'Pick a species';
-    this.fieldTitle = args.fieldTitle;
+    if(this.isReactants) {
+      this.fieldTitle = 'Reactants';
+      this.hookAnchor = 'reactants';
+    }else{
+      this.fieldTitle = 'Products';
+      this.hookAnchor = 'products';
+    }
   },
   render: function () {
     View.prototype.render.apply(this, arguments);
+    if(this.isReactants) {
+      var tooltip = this.parent.parent.tooltips.reactant;
+    }else{
+      var tooltip = this.parent.parent.tooltips.product;
+    }
+    $(this.queryByHook('field-title-tooltip')).prop('title', tooltip);
+    this.renderStoichSpecies();
+    if(this.custom) {
+      $(this.queryByHook(`custom-${this.hookAnchor}`)).css('display', 'block');
+      this.renderSelectSpeciesView();
+      this.toggleAddSpecieButton();
+    }
+  },
+  addSelectedSpecie: function () {
+    var specieName = this.specieName ? this.specieName : 'Pick a variable';
+    if(this.validateAddSpecie()) {
+      this.collection.addStoichSpecie(specieName);
+      this.toggleAddSpecieButton();
+      this.collection.parent.trigger('change-reaction');
+    }
+  },
+  renderSelectSpeciesView: function () {
+    if(this.selectSpeciesView) {
+      this.selectSpeciesView.remove();
+    }
+
+    this.selectSpeciesView = new SelectView({
+      name: 'stoich-specie',
+      required: false,
+      textAttribute: 'name',
+      eagerValidate: false,
+      idAttribute: 'compID',
+      options: this.species,
+      unselectedText: this.unselectedText
+    });
+    app.registerRenderSubview(this, this.selectSpeciesView, `${this.hookAnchor}-select-specie`);
+  },
+  renderStoichSpecies: function () {
     let args = {
       viewOptions: {
         name: 'stoich-specie',
         required: true,
         textAttribute: 'name',
         eagerValidate: true,
-        idAttribute: 'name',
+        idAttribute: 'compID',
+        yieldModel: false,
         options: this.species
       }
     };
-    let type = this.reactionType;
-    let StoichSpeciesView = (type.startsWith('custom')) ? EditCustomStoichSpecieView : EditStoichSpecieView;
     this.renderCollection(
         this.collection,
         StoichSpeciesView,
-        this.queryByHook('reactants-editor'),
+        this.queryByHook(`${this.hookAnchor}-editor`),
         args
     );
-    if(this.reactionType.startsWith('custom')) {
-      $(this.queryByHook('collapse')).collapse();
-    }
-    this.toggleAddSpecieButton();
-    if(this.fieldTitle === "Reactants"){
-      $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.reactant);
-    }else{
-      $(this.queryByHook('field-title-tooltip')).prop('title', this.parent.parent.tooltips.product);
-    }
-  },
-  addSelectedSpecie: function () {
-    var specieName = this.specieName ? this.specieName : 'Pick a variable';
-    if(this.validateAddSpecie()) {
-      this.collection.addStoichSpecie(specieName);
-      this.toggleAddSpecieButton();
-      this.collection.parent.trigger('change-reaction');
-    }
   },
   selectSpecie: function (e) {
     if(this.unselectedText === e.target.selectedOptions.item(0).text){
@@ -90,37 +118,17 @@ module.exports = View.extend({
     this.toggleAddSpecieButton();
   },
   toggleAddSpecieButton: function () {
-    if(!this.validateAddSpecie()){
-      $(this.queryByHook('add-selected-specie')).prop('disabled', true);
-    }else{
-      $(this.queryByHook('add-selected-specie')).prop('disabled', false);
-    }
+    $(this.queryByHook(`${this.hookAnchor}-add-selected-specie`)).prop('disabled', !this.validateAddSpecie());
     this.parent.toggleCustomReactionError();
   },
   validateAddSpecie: function () {
     if(this.hasSelectedSpecie){
       if(!this.collection.length) { return true; }
       if(this.collection.length < 2 && this.collection.at(0).ratio < 2) { return true; }
-      if(this.reactionType !== 'custom-massaction') { return true; }
+      if(this.reactionType === 'custom-propensity') { return true; }
       if(!this.isReactants) { return true; }
       return false;
     }
     return false;
   },
-  subviews: {
-    selectSpecies: {
-      hook: 'select-specie',
-      prepareView: function (el) {
-        return new SelectView({
-          name: 'stoich-specie',
-          required: false,
-          textAttribute: 'name',
-          eagerValidate: false,
-          idAttribute: 'name',
-          options: this.species,
-          unselectedText: this.unselectedText
-        });
-      }
-    }
-  }
 });
\ No newline at end of file

From 034fac2d436c1c6867eae0938180baf52c14f138 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:44:24 -0400
Subject: [PATCH 018/110] Combined the reaction listings and reaction details
 section to allow for a more streamline workflow.

---
 client/model-view/templates/editReaction.pug  |  90 ++++
 .../model-view/templates/reactionDetails.pug  |  27 -
 .../model-view/templates/reactionListing.pug  |  24 -
 client/model-view/views/reaction-details.js   | 239 ---------
 client/model-view/views/reaction-listing.js   | 136 -----
 client/model-view/views/reaction-view.js      | 485 ++++++++++++++++++
 6 files changed, 575 insertions(+), 426 deletions(-)
 create mode 100644 client/model-view/templates/editReaction.pug
 delete mode 100644 client/model-view/templates/reactionDetails.pug
 delete mode 100644 client/model-view/templates/reactionListing.pug
 delete mode 100644 client/model-view/views/reaction-details.js
 delete mode 100644 client/model-view/views/reaction-listing.js
 create mode 100644 client/model-view/views/reaction-view.js

diff --git a/client/model-view/templates/editReaction.pug b/client/model-view/templates/editReaction.pug
new file mode 100644
index 0000000000..0468032826
--- /dev/null
+++ b/client/model-view/templates/editReaction.pug
@@ -0,0 +1,90 @@
+div.mx-1
+
+  if(this.model.collection.indexOf(this.model) !== 0)
+    hr
+
+  div.row.align-items-baseline
+
+    div.col-sm-1
+
+      div.pl-3: input(type="radio" data-hook="select" data-toggle="collapse" data-target="#collapse-reaction-details" + this.model.compID)
+
+    div.col-sm-3(data-hook="input-name-container")
+
+    div.col-sm-4.reaction-list-summary(data-hook="summary")
+
+    div.col-sm-2
+
+      div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="file-alt" class="svg-inline--fa fa-file-alt fa-w-12" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><path fill="currentColor" d="M224 136V0H24C10.7 0 0 10.7 0 24v464c0 13.3 10.7 24 24 24h336c13.3 0 24-10.7 24-24V160H248c-13.2 0-24-10.8-24-24zm64 236c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-64c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-72v8c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm96-114.1v6.1H256V0h6.1c6.4 0 12.5 2.5 17 7l97.9 98c4.5 4.5 7 10.6 7 16.9z"></path></svg>
+
+      button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit
+
+    div.col-sm-2
+
+      button.btn.btn-outline-secondary.box-shadow(data-hook="remove") X
+
+  div.mx-1.pl-2(data-hook="reaction-details")
+
+    div.collapse(id="collapse-reaction-details" + this.model.compID)
+
+      hr
+
+      div.mx-1.row.align-items-baseline
+
+        div.col-sm-6
+
+          div(data-hook="select-reaction-type")
+
+          div
+
+            h5.inline
+
+              span(for="propensity-input") Stochastic Propensity Function:
+
+            div.tooltip-icon(data-html="true" data-hook="rate-parameter-tooltip" data-toggle="tooltip" title=this.parent.tooltips.propensity) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+          div
+
+            div(id="propensity-input" data-hook="propensity-input")
+
+          div
+
+            h5.inline
+
+              span(for="ode-propensity-input") ODE Propensity Function:
+
+            div.tooltip-icon(data-html="true" data-hook="rate-parameter-tooltip" data-toggle="tooltip" title=this.parent.tooltips.odePropensity) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+          div
+
+            div(id="ode-propensity-input" data-hook="ode-propensity-input")
+
+          div.align-self-center
+
+            input.inline.mr-3(type="checkbox" data-hook="mirror-propensities")
+
+            span.inline Same as Stochastic Propensity Function
+
+        div.col-sm-6
+
+          div
+
+            span(for="select-rate-parameter") Rate Parameter:
+
+            div.tooltip-icon(data-html="true" data-hook="rate-parameter-tooltip" data-toggle="tooltip" title=this.parent.tooltips.rate) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+            div.inline.horizontal-space(id="select-rate-parameter" data-hook="select-rate-parameter")
+
+          div.row
+
+            div.col-sm-6(data-hook="reactants-editor")
+
+            div.col-sm-6(data-hook="products-editor")
+
+            div.col-md-12(data-hook="domain-types-editor")
+  
+            div.collapse(data-hook="conflicting-modes-message")
+
+              p.text-warning <b>Warning</b>: This reaction containes Variables with modes of 'Concentration' and 'Population' or 'Hybrid Concentration/Population' and will fire stochastically.
+
+            div(data-hook="custom-reaction-error"): p.text-danger A reaction must have at least one reactant or product
diff --git a/client/model-view/templates/reactionDetails.pug b/client/model-view/templates/reactionDetails.pug
deleted file mode 100644
index 90ad574574..0000000000
--- a/client/model-view/templates/reactionDetails.pug
+++ /dev/null
@@ -1,27 +0,0 @@
-div.row(data-hook="reaction-details")
-
-  div.reaction-summary Summary: 
-
-  div(data-hook="summary-container", id="reaction-summary")
-
-  div.col-md-12(data-hook="select-reaction-type")
-
-  div.col-md-12.verticle-space
-
-    span(for="select-rate-parameter" data-hook="rate-parameter-label")
-
-    div.tooltip-icon(data-html="true" data-hook="rate-parameter-tooltip" data-toggle="tooltip" title="") <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
-
-    div.inline.horizontal-space(id="select-rate-parameter" data-hook="select-rate-parameter")
-
-  div.col-md-12(data-hook="domain-types-editor")
-  
-  div.col-md-6(data-hook="reactants-editor")
-
-  div.col-md-6(data-hook="products-editor")
-
-  div.collapse(data-hook="conflicting-modes-message")
-
-    p.text-warning <b>Warning</b>: This reaction containes Variables with modes of 'Concentration' and 'Population' or 'Hybrid Concentration/Population' and will fire stochastically.
-
-  div(data-hook="custom-reaction-error"): p.text-danger A reaction must have at least one reactant or product
diff --git a/client/model-view/templates/reactionListing.pug b/client/model-view/templates/reactionListing.pug
deleted file mode 100644
index 3b7ea5cae3..0000000000
--- a/client/model-view/templates/reactionListing.pug
+++ /dev/null
@@ -1,24 +0,0 @@
-div.mx-1
-
-  if(this.model.collection.indexOf(this.model) !== 0)
-    hr
-
-  div.row.align-items-baseline
-
-    div.col-md-2
-
-      div.pl-3: input(type="radio" data-hook="select" name="reaction-select")
-
-    div.col-md-2(data-hook="input-name-container")
-
-    div.col-md-3.reaction-list-summary(data-hook="summary")
-
-    div.col-md-3
-
-      div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="file-alt" class="svg-inline--fa fa-file-alt fa-w-12" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><path fill="currentColor" d="M224 136V0H24C10.7 0 0 10.7 0 24v464c0 13.3 10.7 24 24 24h336c13.3 0 24-10.7 24-24V160H248c-13.2 0-24-10.8-24-24zm64 236c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-64c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-72v8c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm96-114.1v6.1H256V0h6.1c6.4 0 12.5 2.5 17 7l97.9 98c4.5 4.5 7 10.6 7 16.9z"></path></svg>
-
-      button.btn.btn-outline-secondary.btn-sm.box-shadow(data-hook="edit-annotation-btn") Edit
-
-    div.col-md-2
-
-      button.btn.btn-outline-secondary.box-shadow(data-hook="remove") X
diff --git a/client/model-view/views/reaction-details.js b/client/model-view/views/reaction-details.js
deleted file mode 100644
index 981b699487..0000000000
--- a/client/model-view/views/reaction-details.js
+++ /dev/null
@@ -1,239 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-let $ = require('jquery');
-let katex = require('katex');
-let _ = require('underscore');
-//support files
-let app = require('../../app');
-let ReactionTypes = require('../../reaction-types');
-//models
-let StoichSpecie = require('../../models/stoich-specie');
-//views
-let InputView = require('../../views/input');
-let View = require('ampersand-view');
-let SelectView = require('ampersand-select-view');
-let ReactionTypesView = require('./reaction-types');
-let ReactantProductView = require('./reactant-product');
-//templates
-let template = require('../templates/reactionDetails.pug');
-
-module.exports = View.extend({
-  template: template,
-  bindings: {
-    'model.propensity': {
-      type: 'value',
-      hook: 'select-rate-parameter'
-    },
-    'model.summary' : {
-      type: function (el, value, previousValue) {
-        katex.render(this.model.summary, this.queryByHook('summary-container'), {
-          displayMode: true,
-          output: 'html'
-        });
-      },
-      hook: 'summary-container',
-    },
-    'model.hasConflict': {
-      type: function (el, value, previousValue) {
-        if(value) {
-          $(this.queryByHook('conflicting-modes-message')).collapse('show');
-        }else{
-          $(this.queryByHook('conflicting-modes-message')).collapse('hide');
-        }
-      },
-      hook: 'conflicting-modes-message'
-    }
-  },
-  events: {
-    'change [data-hook=select-rate-parameter]' : 'selectRateParam',
-    'change [data-hook=select-reaction-type]'  : 'selectReactionType'
-  },
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-    let self = this; 
-    this.model.on("change:reaction_type", function (model) {
-      self.updateStoichSpeciesForReactionType(model.reactionType);
-    });
-  },
-  render: function () {
-    View.prototype.render.apply(this, arguments);
-    let self = this;
-    this.renderReactionTypesSelectView();
-    if(this.model.reactionType === 'custom-propensity'){
-      let propensityView = new InputView({
-        parent: this,
-        required: true,
-        name: 'rate',
-        modelKey:'propensity',
-        valueType: 'string',
-        value: this.model.propensity,
-        placeholder: "--No Expression Entered--"
-      });
-      app.registerRenderSubview(this, propensityView, 'select-rate-parameter');
-      $(this.queryByHook('rate-parameter-label')).text('Propensity:');
-      $(this.queryByHook('rate-parameter-tooltip')).prop('title', this.parent.tooltips.propensity);
-    }else{
-      // make sure the reaction has a rate and that rate exists in the parameters collection
-      let paramIDs = this.model.collection.parent.parameters.map(function (param) {
-        return param.compID;
-      });
-      if(!this.model.rate.compID || !paramIDs.includes(this.model.rate.compID)) {
-        this.model.rate = this.model.collection.getDefaultRate();
-      }
-      let rateParameterView = new SelectView({
-        name: 'rate',
-        required: true,
-        idAttribute: 'cid',
-        textAttribute: 'name',
-        eagerValidate: true,
-        options: this.model.collection.parent.parameters,
-        // For new reactions (with no rate.name) just use the first parameter in the Parameters collection
-        // Else fetch the right Parameter from Parameters based on existing rate
-        value: this.model.rate.name ? this.getRateFromParameters(this.model.rate.name) : this.model.collection.parent.parameters.at(0)
-      });
-      app.registerRenderSubview(this, rateParameterView, 'select-rate-parameter');
-      $(this.queryByHook('rate-parameter-label')).text('Rate Parameter:');
-      $(this.queryByHook('rate-parameter-tooltip')).prop('title', this.parent.tooltips.rate);
-    }
-    let reactantsView = new ReactantProductView({
-      collection: this.model.reactants,
-      species: this.model.collection.parent.species,
-      reactionType: this.model.reactionType,
-      fieldTitle: 'Reactants',
-      isReactants: true
-    });
-    app.registerRenderSubview(this, reactantsView, 'reactants-editor');
-    let productsView = new ReactantProductView({
-      collection: this.model.products,
-      species: this.model.collection.parent.species,
-      reactionType: this.model.reactionType,
-      fieldTitle: 'Products',
-      isReactants: false
-    });
-    app.registerRenderSubview(this, productsView, 'products-editor');
-    if(this.model.collection.parent.is_spatial) {
-      let typesView = new ReactionTypesView({
-        model: this.model,
-        parent: this
-      });
-      app.registerRenderSubview(this, typesView, 'domain-types-editor');
-    }
-    this.totalRatio = this.getTotalReactantRatio();
-    app.tooltipSetup();
-    this.toggleCustomReactionError();
-  },
-  getArrayOfDefaultStoichSpecies: function (arr) {
-    return arr.map(function (params) {
-      let stoichSpecie = new StoichSpecie(params);
-      stoichSpecie.specie = this.parent.getDefaultSpecie();
-      return stoichSpecie;
-    }, this);
-  },
-  getRateFromParameters: function (name) {
-    // Seems like model.rate is not actually part of the Parameters collection
-    // Get the Parameter from Parameters that matches model.rate
-    // TODO this is some garbagio, get model.rate into Parameters collection...?
-    if (!name)  { name = this.model.rate.name };
-    let rate = this.model.collection.parent.parameters.filter(function (param) {
-      return param.name === name;
-    })[0];
-    return rate;
-  },
-  getReactionTypeLabels: function () {
-    return _.map(ReactionTypes, function (val, key) { return val.label; });
-  },
-  getTotalReactantRatio: function () {
-    return this.model.reactants.length;
-  },
-  renderReactionTypes: function () {
-    if(this.model.collection.parent.parameters.length < 1){ return };
-    let options = {
-      displayMode: true,
-      output: 'html'
-    }
-    katex.render(ReactionTypes['creation'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['0'], options);
-    katex.render(ReactionTypes['destruction'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['1'], options);
-    katex.render(ReactionTypes['change'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['2'], options);
-    katex.render(ReactionTypes['dimerization'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['3'], options);
-    katex.render(ReactionTypes['merge'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['4'], options);
-    katex.render(ReactionTypes['split'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['5'], options);
-    katex.render(ReactionTypes['four'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['6'], options);
-  },
-  renderReactionTypesSelectView: function () {
-    if(this.reactionTypesSelectView) {
-      this.reactionTypesSelectView.remove();
-    }
-    if(this.model.collection.parent.parameters.length <= 0){
-      var options = ["Custom propensity"];
-    }
-    else{
-      var options = this.getReactionTypeLabels();
-    }
-    this.reactionTypesSelectView = new SelectView({
-      label: 'Reaction Type:',
-      name: 'reaction-type',
-      required: true,
-      idAttribute: 'cid',
-      options: options,
-      value: ReactionTypes[this.model.reactionType].label
-    });
-    app.registerRenderSubview(this, this.reactionTypesSelectView, 'select-reaction-type');
-    this.renderReactionTypes();
-  },
-  selectRateParam: function (e) {
-    if(this.model.reactionType !== 'custom-propensity') {
-      let val = e.target.selectedOptions.item(0).text;
-      let param = this.getRateFromParameters(val);
-      this.model.rate = param || this.model.rate;
-      this.model.trigger("change");
-      this.model.collection.trigger("change");
-    }
-  },
-  selectReactionType: function (e) {
-    let label = e.target.selectedOptions.item(0).value;
-    let type = _.findKey(ReactionTypes, function (o) { return o.label === label; });
-    this.model.reactionType = type;
-    this.model.summary = label;
-    this.updateStoichSpeciesForReactionType(type);
-    this.model.collection.trigger("change");
-    this.model.trigger('change-reaction');
-    this.render();
-  },
-  toggleCustomReactionError: function () {
-    let errorMsg = $(this.queryByHook("custom-reaction-error"));
-    if(this.model.reactants.length <= 0 && this.model.products.length <= 0) {
-      errorMsg.addClass('component-invalid');
-      errorMsg.removeClass('component-valid');
-    }else{
-      errorMsg.addClass('component-valid');
-      errorMsg.removeClass('component-invalid');
-    }
-  },
-  update: function () {},
-  updateStoichSpeciesForReactionType: function (type) {
-    let args = this.parent.getStoichArgsForReactionType(type);
-    let newReactants = this.getArrayOfDefaultStoichSpecies(args.reactants);
-    let newProducts = this.getArrayOfDefaultStoichSpecies(args.products);
-    this.model.reactants.reset(newReactants);
-    this.model.products.reset(newProducts);
-    if(type !== 'custom-propensity')
-      this.model.rate = this.model.collection.getDefaultRate();
-  },
-  updateValid: function () {}
-});
\ No newline at end of file
diff --git a/client/model-view/views/reaction-listing.js b/client/model-view/views/reaction-listing.js
deleted file mode 100644
index f8f9104774..0000000000
--- a/client/model-view/views/reaction-listing.js
+++ /dev/null
@@ -1,136 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-let $ = require('jquery');
-let katex = require('katex');
-let _ = require('underscore');
-//support files
-let app = require('../../app');
-let tests = require('../../views/tests');
-let modals = require('../../modals');
-//views
-let InputView = require('../../views/input');
-let View = require('ampersand-view');
-//templates
-let viewTemplate = require('../templates/viewReaction.pug');
-let editTemplate = require('../templates/reactionListing.pug');
-
-module.exports = View.extend({
-  bindings: {
-    'model.name' : {
-      type: 'value',
-      hook: 'input-name-container'
-    },
-    'model.summary' : {
-      type: function (el, value, previousValue) {
-        katex.render(this.model.summary, this.queryByHook('summary'), {
-          displayMode: true,
-          output: 'html',
-          maxSize: 5
-        });
-      },
-      hook: 'summary'
-    },
-    'model.selected' : {
-      type: function (el, value, previousValue) {
-        el.checked = value;
-      },
-      hook: 'select'
-    }
-  },
-  events: {
-    'click [data-hook=edit-annotation-btn]' : 'editAnnotation',
-    'click [data-hook=select]'  : 'selectReaction',
-    'click [data-hook=remove]'  : 'removeReaction'
-  },
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-    this.viewMode = attrs.viewMode ? attrs.viewMode : false;
-    if(this.viewMode) {
-      this.rate = this.model.reactionType === "custom-propensity" ? this.model.propensity : this.model.rate.name;
-      this.types = [];
-      let self = this;
-      if(this.model.types) {
-        this.model.types.forEach(function (index) {
-          let type = self.model.collection.parent.domain.types.get(index, "typeID");
-          self.types.push(type.name);
-        });
-      }
-    }else{
-      this.model.on('change', _.bind(this.updateViewer, this));
-    }
-  },
-  render: function () {
-    this.template = this.viewMode ? viewTemplate : editTemplate;
-    View.prototype.render.apply(this, arguments);
-    app.documentSetup();
-    if(!this.model.annotation){
-      $(this.queryByHook('edit-annotation-btn')).text('Add');
-    }
-  },
-  editAnnotation: function () {
-    if(document.querySelector('#reactionAnnotationModal')) {
-      document.querySelector('#reactionAnnotationModal').remove();
-    }
-    let self = this;
-    let name = this.model.name;
-    let annotation = this.model.annotation;
-    let modal = $(modals.annotationModalHtml("reaction", name, annotation)).modal();
-    let okBtn = document.querySelector('#reactionAnnotationModal .ok-model-btn');
-    let input = document.querySelector('#reactionAnnotationModal #reactionAnnotationInput');
-    input.addEventListener("keyup", function (event) {
-      if(event.keyCode === 13){
-        event.preventDefault();
-        okBtn.click();
-      }
-    });
-    okBtn.addEventListener('click', function (e) {
-      self.model.annotation = input.value.trim();
-      self.parent.renderEditReactionListingView();
-      modal.modal('hide');
-    });
-  },
-  removeReaction: function (e) {
-    this.collection.removeReaction(this.model);
-    this.parent.collection.trigger("change");
-  },
-  selectReaction: function (e) {
-    this.model.collection.trigger("select", this.model);
-  },
-  update: function () {},
-  updateValid: function () {},
-  updateViewer: function () {
-    this.parent.renderViewReactionView();
-  },
-  subviews: {
-    inputName: {
-      hook: 'input-name-container',
-      prepareView: function (el) {
-        return new InputView({
-          parent: this,
-          required: true,
-          name: 'name',
-          tests: tests.nameTests,
-          modelKey: 'name',
-          valueType: 'string',
-          value: this.model.name
-        });
-      }
-    }
-  }
-});
\ No newline at end of file
diff --git a/client/model-view/views/reaction-view.js b/client/model-view/views/reaction-view.js
new file mode 100644
index 0000000000..e65857a059
--- /dev/null
+++ b/client/model-view/views/reaction-view.js
@@ -0,0 +1,485 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let katex = require('katex');
+let _ = require('underscore');
+//support files
+let app = require('../../app');
+let modals = require('../../modals');
+let tests = require('../../views/tests');
+let ReactionTypes = require('../../reaction-types');
+//collections
+let StoichSpecies = require('../../models/stoich-species');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+let SelectView = require('ampersand-select-view');
+let RestrictToView = require('./reaction-restrict-to');
+let ReactantProductView = require('./reactant-product');
+//templates
+let viewTemplate = require('../templates/viewReaction.pug');
+let editTemplate = require('../templates/editReaction.pug');
+
+module.exports = View.extend({
+  bindings: {
+    'model.name' : {
+      type: 'value',
+      hook: 'input-name-container'
+    },
+    'model.summary' : {
+      type: function (el, value, previousValue) {
+        katex.render(this.model.summary, this.queryByHook('summary'), {
+          displayMode: true,
+          output: 'html',
+          maxSize: 5
+        });
+      },
+      hook: 'summary'
+    },
+    'model.selected' : {
+      type: function (el, value, previousValue) {
+        el.checked = value;
+      },
+      hook: 'select'
+    },
+    'model.hasConflict': {
+      type: function (el, value, previousValue) {
+        if(value) {
+          $(this.queryByHook('conflicting-modes-message')).collapse('show');
+        }else{
+          $(this.queryByHook('conflicting-modes-message')).collapse('hide');
+        }
+      },
+      hook: 'conflicting-modes-message'
+    },
+    'model.mirrorPropensities': {
+      type: function (el, value, previousValue) {
+        el.checked = value;
+      },
+      hook: 'mirror-propensities'
+    }
+  },
+  events: {
+    'click [data-hook=select]'  : 'selectReaction',
+    'click [data-hook=edit-annotation-btn]' : 'editAnnotation',
+    'click [data-hook=remove]'  : 'removeReaction',
+    'click [data-hook=mirror-propensities]' : 'setMirrorPropensities',
+    'change [data-hook=select-rate-parameter]' : 'selectRateParam',
+    'change [data-hook=propensity-input]' : 'handlePropensityChange',
+    'change [data-hook=select-reaction-type]' : 'selectReactionType'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.viewMode = attrs.viewMode ? attrs.viewMode : false;
+    if(this.viewMode) {
+      this.rate = this.model.reactionType === "custom-propensity" ? this.model.propensity : this.model.rate.name;
+      this.types = [];
+      let self = this;
+      if(this.model.types) {
+        this.model.types.forEach(function (index) {
+          let type = self.model.collection.parent.domain.types.get(index, "typeID");
+          self.types.push(type.name);
+        });
+      }
+    }else{
+      this.model.on('change', _.bind(this.updateViewer, this));
+      this.model.on('change-reaction', () => {
+        if(this.model.massaction) {
+          this.renderODEPropensityInputView({override: true});
+          this.renderPropensityInputView({override: true});
+        }
+      });
+    }
+  },
+  render: function () {
+    this.template = this.viewMode ? viewTemplate : editTemplate;
+    View.prototype.render.apply(this, arguments);
+    if(!this.viewMode){
+      if(this.model.selected) {
+        setTimeout(_.bind(this.openReactionDetails, this), 1);
+      }
+      if(!this.model.annotation){
+        $(this.queryByHook('edit-annotation-btn')).text('Add');
+      }
+    }
+    app.documentSetup();
+  },
+  buildStoichSpecies: function (newSpecs, oldSpecs) {
+    let specIDs = [];
+    newSpecs.forEach((stoichSpecies) => {
+      let index = newSpecs.indexOf(stoichSpecies);
+      if(oldSpecs.at(index)) {
+        stoichSpecies.specie = oldSpecs.at(index).specie;
+      }else{
+        stoichSpecies.specie = this.getSpecies(specIDs);
+      }
+      specIDs.push(stoichSpecies.specie.compID);
+    });
+    return newSpecs;
+  },
+  editAnnotation: function () {
+    if(document.querySelector('#reactionAnnotationModal')) {
+      document.querySelector('#reactionAnnotationModal').remove();
+    }
+    let self = this;
+    let name = this.model.name;
+    let annotation = this.model.annotation;
+    let modal = $(modals.annotationModalHtml("reaction", name, annotation)).modal();
+    let okBtn = document.querySelector('#reactionAnnotationModal .ok-model-btn');
+    let input = document.querySelector('#reactionAnnotationModal #reactionAnnotationInput');
+    input.addEventListener("keyup", function (event) {
+      if(event.keyCode === 13){
+        event.preventDefault();
+        okBtn.click();
+      }
+    });
+    okBtn.addEventListener('click', function (e) {
+      modal.modal('hide');
+      self.model.annotation = input.value.trim();
+      self.parent.renderEditReactionView();
+    });
+  },
+  getReactionTypes: function () {
+    let disableTypes = this.model.collection.parent.parameters.length == 0;
+    let options = _.map(ReactionTypes, function (val, key) {
+      let disabled = disableTypes && key !== "custom-propensity"
+      return [key, val.label, disabled];
+    });
+    return options
+  },
+  getSpecies: function (speciesIDs) {
+    let species = this.model.collection.parent.species.filter((spec) => {
+      return !speciesIDs.includes(spec.compID);
+    });
+    if(species.length > 0) { return species[0]; }
+    return this.model.collection.parent.species.at(0);
+  },
+  handlePropensityChange: function () {
+    if(this.model.mirrorPropensities) {
+      this.model.odePropensity = this.model.propensity;
+      this.renderODEPropensityInputView({override: true});
+    }
+  },
+  openReactionDetails: function () {
+    $("#collapse-reaction-details" + this.model.compID).collapse("show");
+    this.renderDetailsSection();
+  },
+  removeReaction: function (e) {
+    this.collection.removeReaction(this.model);
+    this.parent.collection.trigger("change");
+  },
+  renderDetailsSection: function () {
+    this.renderRateSelectView();
+    this.renderPropensityInputView();
+    this.renderODEPropensityInputView();
+    this.renderReactionTypesSelectView();
+    this.toggleCustomReactionError();
+    this.renderReactantsView();
+    this.renderProductsView();
+    if(this.model.collection.parent.is_spatial) {
+      this.renderRestrictToView()
+    }
+  },
+  renderODEPropensityInputView: function ({override=false}={}) {
+    if(override && this.odePropensityInputView) {
+      this.odePropensityInputView.remove();
+    }
+
+    if(!this.odePropensityInputView || override) {
+      if(this.model.massaction) {
+        var required = false;
+        var propensity = this.model.maODEPropensity
+        var modelKey = 'maODEPropensity'
+        $(this.queryByHook('mirror-propensities')).prop('disabled', true);
+      }else{
+        var required = !this.model.mirrorPropensities;
+        var propensity = this.model.odePropensity
+        var modelKey = 'odePropensity'
+      }
+      
+      this.odePropensityInputView = new InputView({
+        parent: this,
+        required: required,
+        disabled: this.model.massaction || this.model.mirrorPropensities,
+        name: 'ode-propensity',
+        modelKey: modelKey,
+        valueType: 'string',
+        value: propensity,
+        placeholder: "--No Expression Entered--"
+      });
+      app.registerRenderSubview(this, this.odePropensityInputView, 'ode-propensity-input');
+    }
+  },
+  renderProductsView: function ({override=false}={}) {
+    if(override && this.productsView) {
+      this.productsView.remove();
+    }
+
+    if(!this.productsView || override) {
+      this.productsView = new ReactantProductView({
+        collection: this.model.products,
+        species: this.model.collection.parent.species,
+        reactionType: this.model.reactionType,
+        isReactants: false
+      });
+      app.registerRenderSubview(this, this.productsView, 'products-editor');
+    }
+  },
+  renderPropensityInputView: function ({override=false}={}) {
+    if(override && this.propensityInputView) {
+      this.propensityInputView.remove();
+    }
+
+    if(!this.propensityInputView || override) {
+      if(this.model.massaction) {
+        var required = false;
+        var propensity = this.model.maPropensity
+        var modelKey = 'maPropensity'
+      }else{
+        var required = !this.model.odePropensity;
+        var propensity = this.model.propensity
+        var modelKey = 'propensity'
+      }
+      
+      this.propensityInputView = new InputView({
+        parent: this,
+        required: required,
+        disabled: this.model.massaction,
+        name: 'propensity',
+        modelKey: modelKey,
+        valueType: 'string',
+        value: propensity,
+        placeholder: "--No Expression Entered--"
+      });
+      app.registerRenderSubview(this, this.propensityInputView, 'propensity-input');
+    }
+  },
+  renderRateSelectView: function ({override=false}={}) {
+    if(override && this.rateParameterView) {
+      this.rateParameterView.remove();
+    }
+
+    if(!this.rateParameterView || override) {
+      let propensity = this.model.reactionType === 'custom-propensity';
+      viewOptions = {
+        name: 'rate',
+        required: !propensity,
+        idAttribute: 'compID',
+        textAttribute: 'name',
+        eagerValidate: !propensity
+      }
+      if(propensity) {
+        viewOptions['options'] = [];
+        viewOptions['unselectedText'] = "N/A";
+      }else{
+        // make sure the reaction has a rate and that rate exists in the parameters collection
+        let paramIDs = this.model.collection.parent.parameters.map(function (param) {
+          return param.compID;
+        });
+        if(!this.model.rate.compID || !paramIDs.includes(this.model.rate.compID)) {
+          this.model.rate = this.model.collection.getDefaultRate();
+        }
+        viewOptions['options'] = this.model.collection.parent.parameters;
+        viewOptions['value'] = this.model.rate.compID;
+      }
+
+      this.rateParameterView = new SelectView(viewOptions);
+      app.registerRenderSubview(this, this.rateParameterView, 'select-rate-parameter');
+      $(this.queryByHook('select-rate-parameter').firstChild.children[1]).prop('disabled', propensity);
+    }
+  },
+  renderReactantsView: function ({override=false}={}) {
+    if(override && this.reactantsView) {
+      this.reactantsView.remove();
+    }
+
+    if(!this.reactantsView || override) {
+      this.reactantsView = new ReactantProductView({
+        collection: this.model.reactants,
+        species: this.model.collection.parent.species,
+        reactionType: this.model.reactionType,
+        isReactants: true
+      });
+      app.registerRenderSubview(this, this.reactantsView, 'reactants-editor');
+    }
+  },
+  renderReactionTypes: function () {
+    let options = {
+      displayMode: true,
+      output: 'html'
+    }
+    katex.render(ReactionTypes['creation'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['0'], options);
+    katex.render(ReactionTypes['destruction'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['1'], options);
+    katex.render(ReactionTypes['change'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['2'], options);
+    katex.render(ReactionTypes['dimerization'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['3'], options);
+    katex.render(ReactionTypes['merge'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['4'], options);
+    katex.render(ReactionTypes['split'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['5'], options);
+    katex.render(ReactionTypes['four'].label, this.queryByHook('select-reaction-type').firstChild.children[1]['6'], options);
+  },
+  renderReactionTypesSelectView: function ({override=false}={}) {
+    if(override && this.reactionTypesSelectView) {
+      this.reactionTypesSelectView.remove();
+    }
+
+    if(!this.reactionTypesSelectView || override) {
+      let options = this.getReactionTypes();
+      
+      this.reactionTypesSelectView = new SelectView({
+        label: 'Reaction Type:',
+        name: 'reaction-type',
+        required: true,
+        idAttribute: 'cid',
+        options: options,
+        value: this.model.reactionType
+      });
+      app.registerRenderSubview(this, this.reactionTypesSelectView, 'select-reaction-type');
+      this.renderReactionTypes();
+    }
+  },
+  renderRestrictToView: function ({override=true}={}) {
+    if(override && this.restrictToView) {
+      this.restrictToView.remove();
+    }
+
+    if(!this.restrictToView || override) {
+      this.restrictToView = new RestrictToView({
+        model: this.model,
+        parent: this
+      });
+      app.registerRenderSubview(this, this.restrictToView, 'domain-types-editor');
+    }
+  },
+  selectRateParam: function (e) {
+    let val = e.target.selectedOptions.item(0).value;
+    let param = this.model.collection.parent.parameters.get(val, 'compID');
+    if(param) {
+      this.model.rate = param;
+      this.updateViewer();
+      this.model.trigger('change-reaction');
+      this.model.collection.trigger("change");
+    }
+  },
+  selectReaction: function (e) {
+    this.model.selected = !this.model.selected;
+    this.renderDetailsSection();
+  },
+  selectReactionType: function (e) {
+    let oldReactionType = this.model.reactionType;
+    let newReactionType = e.target.selectedOptions.item(0).value;
+    if(newReactionType === 'custom-propensity') {
+      this.model.reactionType = newReactionType;
+      this.model.massaction = false;
+    }else if(newReactionType === 'custom-massaction') {
+      if(oldReactionType === 'custom-propensity') {
+        this.switchCustoms();
+      }else{
+        this.model.reactionType = newReactionType;
+      }
+    }else{
+      this.switchToFormula(newReactionType);
+    }
+    this.model.trigger('change-reaction');
+    if(newReactionType === 'custom-propensity' || oldReactionType === 'custom-propensity') {
+      this.renderRateSelectView({override: true});
+      this.renderPropensityInputView({override: true});
+      this.renderODEPropensityInputView({override: true});
+    }
+    this.renderReactantsView({override: true});
+    this.renderProductsView({override: true});
+  },
+  setMirrorPropensities: function () {
+    this.model.mirrorPropensities = !this.model.mirrorPropensities;
+    if(this.model.mirrorPropensities) {
+      this.prevODEProp = this.model.odePropensity;
+      this.model.odePropensity = this.model.propensity;
+    }else{
+      this.model.odePropensity = Boolean(this.prevODEProp) ? this.prevODEProp : ""
+    }
+    this.renderODEPropensityInputView({override: true});
+  },
+  switchCustoms: function () {
+    let reactants = new StoichSpecies([]);
+    reactants.parent = this.model;
+    var totalRatio = 0;
+    this.model.reactants.forEach((stoichSpecies) => {
+      if(totalRatio < 2) {
+        let ratio = totalRatio + stoichSpecies.ratio > 2 ? 2 - totalRatio : stoichSpecies.ratio;
+        reactants.addStoichSpecie(stoichSpecies.specie.name, {ratio: ratio});
+        totalRatio += ratio;
+      }
+    });
+    this.model.reactionType = 'custom-massaction';
+    this.model.massaction = true;
+    this.model.reactants = reactants;
+    if(!this.model.rate.compID) {
+      this.model.rate = this.model.collection.getDefaultRate();
+    }
+  },
+  switchToFormula: function (reactionType) {
+    let formula = ReactionTypes[reactionType];
+    let reactants = this.buildStoichSpecies(
+      (new StoichSpecies(formula.reactants)), this.model.reactants
+    );
+    reactants.parent = this.model;
+    let products = this.buildStoichSpecies(
+      (new StoichSpecies(formula.products)), this.model.products
+    );
+    products.parent = this.model;
+    this.model.reactionType = reactionType;
+    this.model.massaction = true;
+    this.model.reactants = reactants;
+    this.model.products = products;
+    if(!this.model.rate.compID) {
+      this.model.rate = this.model.collection.getDefaultRate();
+    }
+  },
+  toggleCustomReactionError: function () {
+    let errorMsg = $(this.queryByHook("custom-reaction-error"));
+    if(this.model.reactants.length <= 0 && this.model.products.length <= 0) {
+      errorMsg.addClass('component-invalid');
+      errorMsg.removeClass('component-valid');
+    }else{
+      errorMsg.addClass('component-valid');
+      errorMsg.removeClass('component-invalid');
+    }
+  },
+  update: function () {},
+  updateValid: function () {},
+  updateViewer: function (event) {
+    if(!event || !("selected" in event._changed)){
+      this.parent.renderViewReactionView();
+    }
+  },
+  subviews: {
+    inputName: {
+      hook: 'input-name-container',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'name',
+          tests: tests.nameTests,
+          modelKey: 'name',
+          valueType: 'string',
+          value: this.model.name
+        });
+      }
+    }
+  }
+});
\ No newline at end of file

From d6b06469db1b272142dcd26894a14c47696c3ae8 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:45:20 -0400
Subject: [PATCH 019/110] Refactored to support the new reaction view.

---
 client/model-view/templates/reactionsView.pug |  94 ++++-----
 client/model-view/views/reactions-view.js     | 180 ++++++------------
 2 files changed, 106 insertions(+), 168 deletions(-)

diff --git a/client/model-view/templates/reactionsView.pug b/client/model-view/templates/reactionsView.pug
index c3b6e5b7ef..e32bec78cd 100644
--- a/client/model-view/templates/reactionsView.pug
+++ b/client/model-view/templates/reactionsView.pug
@@ -27,37 +27,31 @@ div#reactions-editor.card
 
       div.tab-pane.active(id="edit-reactions" data-hook="edit-reactions")
 
-        div.row.mb-3
-          
-          div.col-md-7.container-part
-          
-            hr
+        hr
 
-            div.mx-1.row.head.align-items-baseline
+        div.mx-1.row.head.align-items-baseline
+      
+          div.col-sm-1: h6.align-bottom <b>Edit</b>
           
-              div.col-md-2: h6.align-bottom <b>Edit</b>
-              
-              div.col-md-2
-
-                h6.inline <b>Name</b>
+          div.col-sm-3
 
-                div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.name) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+            h6.inline <b>Name</b>
 
-              div.col-md-3: h6 <b>Summary</b>
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.name) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
-              div.col-md-3
+          div.col-sm-4: h6 <b>Summary</b>
 
-                div.inline
+          div.col-sm-2
 
-                  h6 <b>Annotation</b>
+            div.inline
 
-                div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.annotation) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
-              
-              div.col-md-2: h6 <b>Remove</b>
+              h6 <b>Annotation</b>
 
-            div.mt-3(data-hook="edit-reaction-list")
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.annotation) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+          
+          div.col-sm-2: h6 <b>Remove</b>
 
-          div.col-md-5.container-part(data-hook="reaction-details-container")
+        div.mt-3(data-hook="edit-reaction-list")
 
         div(data-hook="massaction-message"): p.text-info To add a mass action reaction the model must have at least one parameter
           
@@ -66,7 +60,7 @@ div#reactions-editor.card
         div.dropdown.inline
 
           button.btn.btn-outline-primary.dropdown-toggle.box-shadow#addReactionBtn(
-            data-hook="add-reaction-full",
+            data-hook="add-reaction",
             data-toggle="dropdown",
             aria-haspopup="true",
             aria-expanded="false",
@@ -74,29 +68,41 @@ div#reactions-editor.card
           ) Add Reaction <span class="caret"></span>
 
           ul.dropdown-menu(aria-labelledby="addReactionBtn")
-            li.dropdown-item(data-hook="creation") <span data-hook=creation-lb1></span><span class=reaction-lb2>Creation Reaction</span>
-            li.dropdown-item(data-hook="destruction") <span data-hook=destruction-lb1></span><span class=reaction-lb2>Destruction Reaction</span>
-            li.dropdown-item(data-hook="change") <span data-hook=change-lb1></span><span class=reaction-lb2>Transformation Reaction</span>
-            li.dropdown-item(data-hook="dimerization") <span data-hook=dimerization-lb1></span><span class=reaction-lb2>Dimerization Reaction</span>
-            li.dropdown-item(data-hook="merge") <span data-hook=merge-lb1></span><span class=reaction-lb2>Merge Reaction</span>
-            li.dropdown-item(data-hook="split") <span data-hook=split-lb1></span><span class=reaction-lb2>Split Reaction</span>
-            li.dropdown-item(data-hook="four") <span data-hook=four-lb1></span><span class=reaction-lb2>Four Reaction</span>
+            li.dropdown-header Mass Action
             li.dropdown-divider
-            li.dropdown-item(data-hook="custom-massaction") Custom mass action
-            li.dropdown-item(data-hook="custom-propensity") Custom propensity
-
-        div.dropdown.inline
-
-          button.btn.btn-outline-primary.dropdown-toggle.box-shadow#addReactionBtn(
-            data-hook="add-reaction-partial",
-            data-toggle="dropdown",
-            aria-haspopup="true",
-            aria-expanded="false",
-            type="button"
-          ) Add Reaction <span class="caret"></span>
-
-          ul.dropdown-menu(aria-labelledby="addReactionBtn")
-            li.dropdown-item(data-hook="custom-propensity") Custom propensity
+            li.dropdown-item.rtype(data-hook="creation")
+              <span data-hook=creation-lb1></span>
+              span.reaction-lb2 Creation Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="destruction")
+              <span data-hook=destruction-lb1></span>
+              span.reaction-lb2 Destruction Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="change")
+              <span data-hook=change-lb1></span>
+              span.reaction-lb2 Transformation Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="dimerization")
+              <span data-hook=dimerization-lb1></span>
+              span.reaction-lb2 Dimerization Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="merge")
+              <span data-hook=merge-lb1></span>
+              span.reaction-lb2 Merge Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="split")
+              <span data-hook=split-lb1></span>
+              span.reaction-lb2 Split Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="four")
+              <span data-hook=four-lb1></span>
+              span.reaction-lb2 Four Reaction
+              span.reaction-lb3 Parameter Required
+            li.dropdown-item.rtype(data-hook="custom-massaction")
+              span Custom Mass Action
+              span.reaction-lb3 Parameter Required
+            li.dropdown-divider
+            li.dropdown-item(data-hook="custom-propensity") Custom Propensity
 
       div.tab-pane(id="view-reactions" data-hook="view-reactions")
 
diff --git a/client/model-view/views/reactions-view.js b/client/model-view/views/reactions-view.js
index 38a00ef305..f0ffd3c0c1 100644
--- a/client/model-view/views/reactions-view.js
+++ b/client/model-view/views/reactions-view.js
@@ -18,33 +18,28 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 let $ = require('jquery');
 let katex = require('katex');
-let _ = require('underscore');
 //support files
 let app = require('../../app');
 let Tooltips = require('../../tooltips');
 let ReactionTypes = require('../../reaction-types');
-//models
-let StoichSpeciesCollection = require('../../models/stoich-species');
 //views
 let View = require('ampersand-view');
-let ViewSwitcher = require('ampersand-view-switcher');
-let ReactionListingView = require('./reaction-listing');
-let ReactionDetailsView = require('./reaction-details');
+let ReactionView = require('./reaction-view');
 //templates
 let template = require('../templates/reactionsView.pug');
 
 module.exports = View.extend({
   template: template,
   events: {
-    'click [data-hook=creation]'               : 'handleAddReactionClick',
-    'click [data-hook=destruction]'            : 'handleAddReactionClick',
-    'click [data-hook=change]'                 : 'handleAddReactionClick',
-    'click [data-hook=dimerization]'           : 'handleAddReactionClick',
-    'click [data-hook=merge]'                  : 'handleAddReactionClick',
-    'click [data-hook=split]'                  : 'handleAddReactionClick',
-    'click [data-hook=four]'                   : 'handleAddReactionClick',
-    'click [data-hook=custom-massaction]'      : 'handleAddReactionClick',
-    'click [data-hook=custom-propensity]'      : 'handleAddReactionClick',
+    'click [data-hook=creation]' : 'handleAddReactionClick',
+    'click [data-hook=destruction]' : 'handleAddReactionClick',
+    'click [data-hook=change]' : 'handleAddReactionClick',
+    'click [data-hook=dimerization]' : 'handleAddReactionClick',
+    'click [data-hook=merge]' : 'handleAddReactionClick',
+    'click [data-hook=split]' : 'handleAddReactionClick',
+    'click [data-hook=four]' : 'handleAddReactionClick',
+    'click [data-hook=custom-massaction]' : 'handleAddReactionClick',
+    'click [data-hook=custom-propensity]' : 'handleAddReactionClick',
     'click [data-hook=collapse]' : 'changeCollapseButtonText'
   },
   initialize: function (attrs, options) {
@@ -52,31 +47,14 @@ module.exports = View.extend({
     this.tooltips = Tooltips.reactionsEditor;
     this.readOnly = attrs.readOnly ? attrs.readOnly : false;
     if(!this.readOnly) {
-      this.collection.on("select", function (reaction) {
-        this.setSelectedReaction(reaction);
-        this.setDetailsView(reaction);
-      }, this);
-      this.collection.on("remove", function (reaction) {
-        // Select the last reaction by default
-        // But only if there are other reactions other than the one we're removing
-        if (reaction.detailsView){
-          reaction.detailsView.remove();
-        }
-        this.collection.removeReaction(reaction);
-        if (this.collection.length) {
-          let selected = this.collection.at(this.collection.length-1);
-          this.collection.trigger("select", selected);
-        }
-      }, this);
       this.collection.parent.species.on('add remove', this.toggleAddReactionButton, this);
-      this.collection.parent.parameters.on('add remove', this.toggleReactionTypes, this);
+      this.collection.parent.parameters.on('add remove', this.updateMAState, this);
       this.collection.parent.on('change', this.toggleProcessError, this);
     }
   },
   render: function () {
     View.prototype.render.apply(this, arguments);
     if(this.readOnly) {
-      this.renderViewReactionView();
       $(this.queryByHook('reactions-edit-tab')).addClass("disabled");
       $(".nav .disabled>a").on("click", function(e) {
         e.preventDefault();
@@ -86,41 +64,34 @@ module.exports = View.extend({
       $(this.queryByHook('edit-reactions')).removeClass('active');
       $(this.queryByHook('view-reactions')).addClass('active');
     }else{
-      this.renderReactionListingViews();
-      if (this.collection.length) {
-        this.setSelectedReaction(this.collection.at(0));
-        this.collection.trigger("select", this.selectedReaction);
-      }
+      this.renderEditReactionView();
       this.toggleAddReactionButton();
-      if(this.collection.parent.parameters.length > 0){
-         $(this.queryByHook('add-reaction-partial')).prop('hidden', true);
-      }else {
-        $(this.queryByHook('add-reaction-full')).prop('hidden', true);
-      }
+      this.updateMAState();
       this.renderReactionTypes();
-      katex.render("\\emptyset", this.queryByHook('emptyset'), {
-        displayMode: false,
-        output: 'html',
-      });
       this.toggleProcessError();
-      $(this.queryByHook('massaction-message')).prop('hidden', this.collection.parent.parameters.length > 0);
     }
+    katex.render("\\emptyset", this.queryByHook('emptyset'), {
+      displayMode: false,
+      output: 'html',
+    });
+    this.renderViewReactionView();
   },
   changeCollapseButtonText: function (e) {
     app.changeCollapseButtonText(this, e);
   },
-  getAnnotation: function (type) {
-    return ReactionTypes[type].label;
-  },
-  getDefaultSpecie: function () {
-    return this.collection.parent.species.models[0];
-  },
   getStoichArgsForReactionType: function(type) {
     return ReactionTypes[type];
   },
   handleAddReactionClick: function (e) {
+    let disableTypes = this.collection.parent.parameters.length == 0;
+    let maTypes = [
+      "creation", "destruction", "change", "dimerization",
+      "merge", "split", "four", "custom-massaction"
+    ]
     let reactionType = e.delegateTarget.dataset.hook;
-    let stoichArgs = this.getStoichArgsForReactionType(reactionType);
+    if(disableTypes && maTypes.includes(reactionType)) {
+      return
+    }
     if(this.parent.model.domain.types) {
       var types = this.parent.model.domain.types.map(function (type) {
         return type.typeID;
@@ -129,20 +100,10 @@ module.exports = View.extend({
     }else{
       var types = [];
     }
+    let stoichArgs = this.getStoichArgsForReactionType(reactionType);
     let reaction = this.collection.addReaction(reactionType, stoichArgs, types);
-    reaction.detailsView = this.newDetailsView(reaction);
-    this.collection.trigger("select", reaction);
     app.tooltipSetup();
-  },
-  newDetailsView: function (reaction) {
-    let detailsView = new ReactionDetailsView({ model: reaction });
-    detailsView.parent = this;
-    return detailsView;
-  },
-  openReactionsContainer: function () {
-    $(this.queryByHook('reactions-list-container')).collapse('show');
-    let collapseBtn = $(this.queryByHook('collapse'));
-    collapseBtn.trigger('click');
+    this.collection.trigger('change');
   },
   openSection: function (error, {isCollection=false}={}) {
     if(!$(this.queryByHook("reactions-list-container")).hasClass("show")) {
@@ -152,34 +113,24 @@ module.exports = View.extend({
     }
     app.switchToEditTab(this, "reactions");
     if(error.type !== "process") {
-      let reaction = this.collection.filter((react) => {
-        return react.compID === error.id;
+      let reactionView = this.editReactionView.views.filter((reactView) => {
+        return reactView.model.compID === error.id;
       })[0];
-      this.collection.trigger("select", reaction);
+      reactionView.model.selected = true;
+      reactionView.openReactionDetails();
     }
   },
-  renderEditReactionListingView: function () {
-    if(this.editReactionListingView){
-      this.editReactionListingView.remove();
+  renderEditReactionView: function () {
+    if(this.editReactionView){
+      this.editReactionView.remove();
     }
-    if(this.collection.parent.parameters.length <= 0) {
-      for(var i = 0; i < this.collection.length; i++) {
-        if(this.collection.models[i].reactionType !== "custom-propensity"){
-          this.collection.models[i].reactionType = "custom-propensity";
-        }
-      }
-    }
-    this.editReactionListingView = this.renderCollection(
+    this.editReactionView = this.renderCollection(
       this.collection,
-      ReactionListingView,
+      ReactionView,
       this.queryByHook('edit-reaction-list')
     );
     app.tooltipSetup();
   },
-  renderReactionListingViews: function () {
-    this.renderEditReactionListingView();
-    this.renderViewReactionView();
-  },
   renderReactionTypes: function () {
     let options = {
       displayMode: false,
@@ -194,8 +145,8 @@ module.exports = View.extend({
     katex.render(ReactionTypes['four'].label, this.queryByHook('four-lb1'), options);
   },
   renderViewReactionView: function () {
-    if(this.viewReactionListingView){
-      this.viewReactionListingView.remove();
+    if(this.viewReactionView){
+      this.viewReactionView.remove();
     }
     if(!this.collection.parent.is_spatial){
       $(this.queryByHook("reaction-types-header")).css("display", "none");
@@ -207,25 +158,15 @@ module.exports = View.extend({
       $(this.queryByHook("reaction-annotation-header")).css("display", "block");
     }
     let options = {viewOptions: {viewMode: true, hasAnnotations: this.containsMdlWithAnn}}
-    this.viewReactionListingView = this.renderCollection(
+    this.viewReactionView = this.renderCollection(
       this.collection,
-      ReactionListingView,
+      ReactionView,
       this.queryByHook('view-reaction-list'),
       options
     );
   },
-  setDetailsView: function (reaction) {
-    reaction.detailsView = this.newDetailsView(reaction);
-    this.detailsViewSwitcher.set(reaction.detailsView);
-  },
-  setSelectedReaction: function (reaction) {
-    this.collection.each(function (m) { m.selected = false; });
-    reaction.selected = true;
-    this.selectedReaction = reaction;
-  },
   toggleAddReactionButton: function () {
-    $(this.queryByHook('add-reaction-full')).prop('disabled', (this.collection.parent.species.length <= 0));
-    $(this.queryByHook('add-reaction-partial')).prop('disabled', (this.collection.parent.species.length <= 0));
+    $(this.queryByHook('add-reaction')).prop('disabled', (this.collection.parent.species.length <= 0));
   },
   toggleProcessError: function () {
     let model = this.collection.parent;
@@ -239,30 +180,21 @@ module.exports = View.extend({
       errorMsg.removeClass('component-invalid');
     }
   },
-  toggleReactionTypes: function (e, prev, curr) {
-    if(curr && curr.add && this.collection.parent.parameters.length === 1){
-      $(this.queryByHook('massaction-message')).prop('hidden', true);
-      $(this.queryByHook('add-reaction-full')).prop('hidden', false);
-      $(this.queryByHook('add-reaction-partial')).prop('hidden', true);
-    }else if(curr && !curr.add && this.collection.parent.parameters.length === 0){
-      $(this.queryByHook('massaction-message')).prop('hidden', false);
-      $(this.queryByHook('add-reaction-full')).prop('hidden', true);
-      $(this.queryByHook('add-reaction-partial')).prop('hidden', false);
-    }
-    if(this.selectedReaction){
-      this.selectedReaction.detailsView.renderReactionTypesSelectView();
-    }
-  },
   update: function () {},
-  updateValid: function () {},
-  subviews: {
-    detailsViewSwitcher: {
-      hook: "reaction-details-container",
-      prepareView: function (el) {
-        return new ViewSwitcher({
-          el: el
-        });
+  updateMAState: function () {
+    let disableTypes = this.collection.parent.parameters.length == 0;
+    let maTypes = [
+      "creation", "destruction", "change", "dimerization",
+      "merge", "split", "four", "custom-massaction"
+    ]
+    for(var i = 0; i < maTypes.length; i++) {
+      if(disableTypes) {
+        $(this.queryByHook(maTypes[i])).addClass("disabled")
+      }else{
+        $(this.queryByHook(maTypes[i])).removeClass("disabled")
       }
     }
-  }
+    $(this.queryByHook('massaction-message')).prop('hidden', !disableTypes);
+  },
+  updateValid: function () {},
 });
\ No newline at end of file

From 2694288a01cbc46466d2a663d751d0219c84cea6 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:47:10 -0400
Subject: [PATCH 020/110] Reactored the event listeners to be compatable with
 the changes to reactions.

---
 client/model-view/views/parameters-view.js |  3 +++
 client/model-view/views/species-view.js    | 12 +++++-------
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/client/model-view/views/parameters-view.js b/client/model-view/views/parameters-view.js
index 4dc463bb68..c9c95b6e9b 100644
--- a/client/model-view/views/parameters-view.js
+++ b/client/model-view/views/parameters-view.js
@@ -41,6 +41,9 @@ module.exports = View.extend({
       self.collection.parent.reactions.map(function (reaction) {
         if(reaction.rate && reaction.rate.compID === compID){
           reaction.rate = parameter;
+          if(reaction.reactionType !== 'custom-propensity') {
+            reaction.trigger('change-reaction');
+          }
         }
       });
       self.collection.parent.eventsCollection.map(function (event) {
diff --git a/client/model-view/views/species-view.js b/client/model-view/views/species-view.js
index f9fa717277..a00e004cdb 100644
--- a/client/model-view/views/species-view.js
+++ b/client/model-view/views/species-view.js
@@ -42,23 +42,21 @@ module.exports = View.extend({
     let self = this;
     this.collection.on('update-species', function (compID, specie, isNameUpdate, isDefaultMode) {
       self.collection.parent.reactions.forEach(function (reaction) {
+        var changedReaction = false;
         reaction.reactants.forEach(function (reactant) {
           if(reactant.specie.compID === compID) {
             reactant.specie = specie;
+            changedReaction = true;
           }
         });
         reaction.products.forEach(function (product) {
           if(product.specie.compID === compID) {
             product.specie = specie;
+            changedReaction = true;
           }
         });
-        if(isNameUpdate) {
-          reaction.buildSummary();
-          if(reaction.selected) {
-            self.parent.reactionsView.setDetailsView(reaction);
-          }
-        }else if(!isDefaultMode || specie.compID === self.collection.models[self.collection.length-1].compID){
-          reaction.checkModes();
+        if(changedReaction) {
+          reaction.trigger('change-reaction');
         }
       });
       self.collection.parent.eventsCollection.forEach(function (event) {

From 6ad6e66ec473880c72867832c3ebceef06dcb818 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 12:50:56 -0400
Subject: [PATCH 021/110] Updated GillesPy2 to v1.6.10 and SpatialPy to v1.0.3.

---
 requirements.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 8d02090cff..100e866b42 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,6 +2,6 @@ python-libsbml==5.18.0
 python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
-gillespy2==1.6.9
-spatialpy==1.0.2
+gillespy2==1.6.10
+spatialpy==1.0.3
 git+https://github.com/StochSS/sciope.git@master

From c5d0e56296fdc1a3df0b17861722f939730f6955 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 14:09:39 -0400
Subject: [PATCH 022/110] Fixed issue with the mirror propensities checkbox
 remaining disabled when switching to custom propensity reactions.

---
 client/model-view/views/reaction-view.js | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/client/model-view/views/reaction-view.js b/client/model-view/views/reaction-view.js
index e65857a059..30f8042e32 100644
--- a/client/model-view/views/reaction-view.js
+++ b/client/model-view/views/reaction-view.js
@@ -204,13 +204,14 @@ module.exports = View.extend({
     if(!this.odePropensityInputView || override) {
       if(this.model.massaction) {
         var required = false;
-        var propensity = this.model.maODEPropensity
-        var modelKey = 'maODEPropensity'
+        var propensity = this.model.maODEPropensity;
+        var modelKey = 'maODEPropensity';
         $(this.queryByHook('mirror-propensities')).prop('disabled', true);
       }else{
         var required = !this.model.mirrorPropensities;
-        var propensity = this.model.odePropensity
-        var modelKey = 'odePropensity'
+        var propensity = this.model.odePropensity;
+        var modelKey = 'odePropensity';
+        $(this.queryByHook('mirror-propensities')).prop('disabled', false);
       }
       
       this.odePropensityInputView = new InputView({

From e67a9a85abc08454f7b97dd4dcf92d1b7221d51a Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 22 Jun 2022 14:11:53 -0400
Subject: [PATCH 023/110] Fixed improper refs to reactionType.

---
 stochss/handlers/util/stochss_model.py         | 2 +-
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/stochss/handlers/util/stochss_model.py b/stochss/handlers/util/stochss_model.py
index 0bbe55baa4..0f9ec2bdbd 100644
--- a/stochss/handlers/util/stochss_model.py
+++ b/stochss/handlers/util/stochss_model.py
@@ -162,7 +162,7 @@ def __convert_reactions(self, model):
         try:
             g_parameters = model.get_all_parameters()
             for reaction in self.model['reactions']:
-                if reaction['reactionType'] == "custom-propensity":
+                if not reaction['massaction']:
                     rate = None
                     propensity = reaction['propensity']
                     ode_propensity = reaction['odePropensity']
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 4b9b0cf513..bcac112574 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -243,7 +243,7 @@ def __convert_reactions(self, model, type_ids):
             for reaction in self.model['reactions']:
                 reactants, products = self.__convert_stoich_species(model=model,
                                                                     reaction=reaction)
-                if reaction['reactionType'] != "custom-propensity":
+                if reaction['massaction']:
                     rate = s_params[reaction['rate']['name']]
                     propensity = None
                     ode_propensity = None

From a30ef10f5215605c33cb4018e82a2abd2743fe98 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 23 Jun 2022 07:16:11 -0400
Subject: [PATCH 024/110] Replaced the modelStateButtons ref remnant with the
 correct parent ref.

---
 client/model-view/views/domain-viewer.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/model-view/views/domain-viewer.js b/client/model-view/views/domain-viewer.js
index 04b83f3fdc..90b1f5a373 100644
--- a/client/model-view/views/domain-viewer.js
+++ b/client/model-view/views/domain-viewer.js
@@ -274,7 +274,7 @@ module.exports = View.extend({
   },
   saveDomainToModel: function (e) {
     this.parent.model.domain = this.model;
-    this.parent.modelStateButtons.clickSaveHandler(e);
+    this.parent.parent.clickSaveHandler(e);
     this.reloadDomain();
   },
   selectParticle: function (data) {

From 5cd782cbfa323fd89332d1962744f700966c002e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 23 Jun 2022 18:27:27 -0400
Subject: [PATCH 025/110] Refactored the get_domain_plot function to be an
 instance method and to accept a tuple of domain objects to use when building
 the domain plot.  refactored the get_particles_from_3D_domain to generate and
 return a domain plot if the client doesn't have it.  Fixed issue with type
 ref in spatialpy domain.

---
 .../handlers/util/stochss_spatial_model.py    | 38 +++++++++++--------
 1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index a32a083a4f..8b63102abf 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -122,7 +122,7 @@ def __build_stochss_domain_particles(cls, s_domain, data=None):
             if data is None or data['type'] is None:
                 viscosity = s_domain.nu[i]
                 fixed = bool(s_domain.fixed[i])
-                type_id = int(s_domain.type[i])
+                type_id = s_domain.typeNdxMapping[s_domain.type_id[i]]
             else:
                 viscosity = data['type']['nu']
                 fixed = data['type']['fixed']
@@ -462,7 +462,7 @@ def get_domain(self, path=None, new=False):
         return self.__load_domain_from_file(path=path)
 
 
-    def get_domain_plot(self, path=None, new=False):
+    def get_domain_plot(self, path=None, new=False, domains=None):
         '''
         Get a plotly plot of the models domain or a prospective domain
 
@@ -472,20 +472,25 @@ def get_domain_plot(self, path=None, new=False):
             Path to a prospective domain
         new : bool
             Indicates whether or not to load an new domain
+        domains : tuple(spatialpy.Domain, stochss.Domain)
+            Domain objects used to generate plot data.
         '''
-        if new:
-            path = '/stochss/stochss_templates/nonSpatialModelTemplate.json'
-        elif path is None:
-            path = self.path
-        try:
-            domain = Domain.read_stochss_domain(path)
-        except DomainError as err:
-            raise DomainFormatError(f"Failed to load the domain.  Reason given: {err}") from err
+        if domains is None:
+            if new:
+                path = '/stochss/stochss_templates/nonSpatialModelTemplate.json'
+            elif path is None:
+                path = self.path
+            try:
+                domain = Domain.read_stochss_domain(path)
+            except DomainError as err:
+                raise DomainFormatError(f"Failed to load the domain.  Reason given: {err}") from err
+        else:
+            domain = domains[0]
         fig = domain.plot_types(return_plotly_figure=True)
         if not fig['data']:
             fig['data'].append(self.__get_trace_data(particles=[], name="Un-Assigned"), index=0)
         else:
-            s_domain = self.load()['domain']
+            s_domain = self.load()['domain'] if domains is None else domains[1]
             for i, d_type in enumerate(s_domain['types']):
                 if len(s_domain['types']) > 1:
                     particles = list(filter(lambda particle, key=i: particle['type'] == key,
@@ -526,8 +531,7 @@ def get_notebook_data(self):
         return {"path":path, "new":True, "models":{"s_model":self.model, "model":s_model}}
 
 
-    @classmethod
-    def get_particles_from_3d_domain(cls, data):
+    def get_particles_from_3d_domain(self, data):
         '''
         Create a new 3D domain and return the particles
 
@@ -553,9 +557,13 @@ def get_particles_from_3d_domain(cls, data):
         else:
             s_domain = Domain.create_2D_domain(xlim=xlim, ylim=ylim,
                                                nx=data['nx'], ny=data['ny'], **data['type'])
-        domain = cls.__build_stochss_domain(s_domain=s_domain)
+        domain = self.__build_stochss_domain(s_domain=s_domain)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
-        return {"particles":domain['particles'], "limits":limits}
+        resp = {"particles":domain['particles'], "limits":limits}
+        if data['domainExists']:
+            return resp
+        resp['figure'] = json.loads(self.get_domain_plot(domains=(s_domain, domain)))
+        return resp
 
 
     @classmethod

From 7dc7d9b980c07abc4e47bb7abb6a106b4031f8c1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 23 Jun 2022 18:33:39 -0400
Subject: [PATCH 026/110] Refactored the Create3DDomain api handler to use the
 refactored get_particles_from_3D_domain method.

---
 stochss/handlers/models.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 851742ada3..2dd2ab7d9a 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -375,7 +375,8 @@ async def post(self):
         log.debug("Data used to create the domain: {data}")
         try:
             log.info("Generating new particles")
-            resp = StochSSSpatialModel.get_particles_from_3d_domain(data=data)
+            model = StochSSSpatialModel(path="")
+            resp = model.get_particles_from_3d_domain(data=data)
             log.debug(f"Number of Particles: {len(resp['particles'])}")
             log.info("Successfully created new particles")
             self.write(resp)

From f3da85bccda3304a9bce6d40de0e51560b9c501f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 23 Jun 2022 18:36:40 -0400
Subject: [PATCH 027/110] Refactored the handle build domain function to allow
 it to work correctly when no domain plot exists.

---
 client/views/edit-3D-domain.js | 55 +++++++++++++++++++++-------------
 1 file changed, 35 insertions(+), 20 deletions(-)

diff --git a/client/views/edit-3D-domain.js b/client/views/edit-3D-domain.js
index 03c5afff1a..af6c0b404d 100644
--- a/client/views/edit-3D-domain.js
+++ b/client/views/edit-3D-domain.js
@@ -38,7 +38,7 @@ module.exports = View.extend({
   },
   handleBuildDomain: function (e) {
     this.startAction("Creating domain ...")
-    this.data.type = {"type_id":this.type.typeID, "mass":this.type.mass, "nu":this.type.nu, "fixed":this.type.fixed};
+    this.data.type = {"type_id":this.type.name, "mass":this.type.mass, "nu":this.type.nu, "fixed":this.type.fixed};
     this.data.volume = this.type.volume;
     let xtrans = Number($(this.queryByHook("domain-x-trans")).find('input')[0].value);
     let ytrans = Number($(this.queryByHook("domain-y-trans")).find('input')[0].value);
@@ -46,30 +46,45 @@ module.exports = View.extend({
     if(xtrans !== 0 || ytrans !== 0 || ztrans !== 0) {
       this.data.transformation = [xtrans, ytrans, ztrans];
     }
+    this.data.domainExists = Boolean(this.parent.plot);
     let self = this;
     let endpoint = path.join(app.getApiPath(), "spatial-model/3d-domain");
     app.postXHR(endpoint, this.data, {
       success: function (err, response, body) {
-        self.parent.addParticles(body.particles);
-        if(self.parent.domain.x_lim[0] > body.limits.x_lim[0]) {
-          self.parent.domain.x_lim[0] = body.limits.x_lim[0];
+        if(self.data.domainExists) {
+          self.parent.addParticles(body.particles);
+          if(self.parent.domain.x_lim[0] > body.limits.x_lim[0]) {
+            self.parent.domain.x_lim[0] = body.limits.x_lim[0];
+          }
+          if(self.parent.domain.y_lim[0] > body.limits.y_lim[0]) {
+            self.parent.domain.y_lim[0] = body.limits.y_lim[0];
+          }
+          if(self.parent.domain.z_lim[0] > body.limits.z_lim[0]) {
+            self.parent.domain.z_lim[0] = body.limits.z_lim[0];
+          }
+          if(self.parent.domain.x_lim[1] < body.limits.x_lim[1]) {
+            self.parent.domain.x_lim[1] = body.limits.x_lim[1];
+          }
+          if(self.parent.domain.y_lim[1] < body.limits.y_lim[1]) {
+            self.parent.domain.y_lim[1] = body.limits.y_lim[1];
+          }
+          if(self.parent.domain.z_lim[1] < body.limits.z_lim[1]) {
+            self.parent.domain.z_lim[1] = body.limits.z_lim[1];
+          }
+          self.parent.renderDomainLimitations();
+        }else{
+          self.parent.domain.x_lim = body.limits.x_lim;
+          self.parent.domain.y_lim = body.limits.y_lim;
+          self.parent.domain.z_lim = body.limits.z_lim;
+          body.particles.forEach((particle) => {
+            self.parent.domain.particles.addParticle(
+              particle.point, particle.volume, particle.mass, particle.type, particle.nu, particle.fixed
+            );
+          });
+          self.parent.plot = body.figure;
+          self.parent.renderDomainLimitations();
+          self.parent.displayDomain();
         }
-        if(self.parent.domain.y_lim[0] > body.limits.y_lim[0]) {
-          self.parent.domain.y_lim[0] = body.limits.y_lim[0];
-        }
-        if(self.parent.domain.z_lim[0] > body.limits.z_lim[0]) {
-          self.parent.domain.z_lim[0] = body.limits.z_lim[0];
-        }
-        if(self.parent.domain.x_lim[1] < body.limits.x_lim[1]) {
-          self.parent.domain.x_lim[1] = body.limits.x_lim[1];
-        }
-        if(self.parent.domain.y_lim[1] < body.limits.y_lim[1]) {
-          self.parent.domain.y_lim[1] = body.limits.y_lim[1];
-        }
-        if(self.parent.domain.z_lim[1] < body.limits.z_lim[1]) {
-          self.parent.domain.z_lim[1] = body.limits.z_lim[1];
-        }
-        self.parent.renderDomainLimitations();
         self.completeAction("Domain successfully created");
         $('html, body').animate({
             scrollTop: $("#domain-plot").offset().top

From d07a7960f7caa0426ef1e6b03781036864b4a379 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Fri, 24 Jun 2022 15:24:19 -0400
Subject: [PATCH 028/110] Added block to handle the unsupported '-' in the
 'Un-Assigned' type.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 8b63102abf..be9b708eac 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -540,6 +540,8 @@ def get_particles_from_3d_domain(self, data):
         data : dict
             Data used to create the 3D domain
         '''
+        if data['type']['type_id'] == "Un-Assigned":
+            data['type']['type_id'] = "UnAssigned"
         if data['transformation'] is None:
             xlim = data['xLim']
             ylim = data['yLim']

From 5f6f49551607ae79c3559504a47a3f0575665080 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Jun 2022 13:40:12 -0400
Subject: [PATCH 029/110] Added checks in model editor and domain viewer to
 properly inform users when a domain has no particles to plot.

---
 client/model-view/views/domain-viewer.js | 20 +++++++++++++-------
 client/pages/model-editor.js             |  1 +
 client/templates/pages/modelEditor.pug   |  2 ++
 3 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/client/model-view/views/domain-viewer.js b/client/model-view/views/domain-viewer.js
index 90b1f5a373..ac4ec74f3d 100644
--- a/client/model-view/views/domain-viewer.js
+++ b/client/model-view/views/domain-viewer.js
@@ -154,13 +154,15 @@ module.exports = View.extend({
   },
   reloadDomain: function (domainPath) {
     if(this.domainPath !== domainPath || domainPath === "viewing") {
-      let el = this.elements === null ? this.queryByHook("view-domain-plot") : this.elements.plot;
-      el.removeListener('plotly_click', this.selectParticle);
-      Plotly.purge(el);
-      this.plot = null;
-      this.model.types.forEach(function (type) {
-        type.numParticles = 0;
-      });
+      if(this.plot) {
+        let el = this.elements === null ? this.queryByHook("view-domain-plot") : this.elements.plot;
+        el.removeListener('plotly_click', this.selectParticle);
+        Plotly.purge(el);
+        this.plot = null;
+        this.model.types.forEach(function (type) {
+          type.numParticles = 0;
+        });
+      }
       this.parent.renderDomainViewer(domainPath);
     }
   },
@@ -227,6 +229,10 @@ module.exports = View.extend({
     }
   },
   renderPlot: function (plotElement) {
+    if(this.model.particles.length <= 0) {
+      return
+    }
+    $(this.parent.domainElements.plotEmpty).css('display', 'none');
     if(this.plot === null) {
       let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
       app.getXHR(endpoint, {
diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
index fe16d3b4dc..f473f368a1 100644
--- a/client/pages/model-editor.js
+++ b/client/pages/model-editor.js
@@ -331,6 +331,7 @@ let ModelEditor = PageView.extend({
       select: $(this.queryByHook("me-select-particle")),
       particle: {view: this, hook: "me-particle-viewer"},
       plot: this.queryByHook("domain-plot-container"),
+      plotEmpty: this.queryByHook("domain-plot-container-empty"),
       type: this.queryByHook("me-types-quick-view")
     }
     this.modelView = new ModelView({
diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug
index 5f5f5f9fc9..2031b051b8 100644
--- a/client/templates/pages/modelEditor.pug
+++ b/client/templates/pages/modelEditor.pug
@@ -37,6 +37,8 @@ section.page
 
           div(data-hook="domain-plot-container")
 
+          div.text-danger(data-hook="domain-plot-container-empty") The domain currently has no particles to display
+
         div.col-sm-4.overflow-auto(style="max-height:450px;")
 
           div.mt-2.particle-view(data-hook="me-particle-viewer")

From 02e6783b3e2d49b6ef62a1325bf99faa6b116fcc Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Jun 2022 13:43:52 -0400
Subject: [PATCH 030/110] Added checks in the domain editor to properly inform
 users when a domain has no particles to plot.

---
 client/pages/domain-editor.js           | 23 +++++++++++++++--------
 client/templates/pages/domainEditor.pug |  2 ++
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/client/pages/domain-editor.js b/client/pages/domain-editor.js
index acbe54f347..3c4d84e8a3 100644
--- a/client/pages/domain-editor.js
+++ b/client/pages/domain-editor.js
@@ -410,7 +410,10 @@ let DomainEditor = PageView.extend({
     this.updatePlot();
   },
   displayDomain: function () {
-    let self = this;
+    if(!this.plot) {
+      return
+    }
+    $(this.queryByHook("domain-plot-empty")).css('display', 'none');
     var el = this.queryByHook("domain-plot");
     Plotly.newPlot(el, this.plot);
     el.on('plotly_click', _.bind(this.selectParticle, this));
@@ -706,13 +709,17 @@ let DomainEditor = PageView.extend({
     this.renderTypesFileSelect();
     this.renderCreate3DDomain();
     let self = this;
-    let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
-    app.getXHR(endpoint, {
-      success: function (err, response, body) {
-        self.plot = body.fig;
-        self.displayDomain();
-      }
-    });
+    if(this.domain.particles.length > 0) {
+      let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
+      app.getXHR(endpoint, {
+        success: function (err, response, body) {
+          self.plot = body.fig;
+          self.displayDomain();
+        }
+      });
+    }else{
+      this.displayDomain();
+    }
     $(document).ready(function () {
       $('[data-toggle="tooltip"]').tooltip();
       $('[data-toggle="tooltip"]').click(function () {
diff --git a/client/templates/pages/domainEditor.pug b/client/templates/pages/domainEditor.pug
index 578b0d59bb..8d361c67b0 100644
--- a/client/templates/pages/domainEditor.pug
+++ b/client/templates/pages/domainEditor.pug
@@ -298,6 +298,8 @@ section.page
 
       div(id="domain-plot" data-hook="domain-plot" style="height: 800px")
 
+      div.text-danger(data-hook="domain-plot-empty") The domain currently has no particles to display
+
   div.inline
 
     button.btn.btn-primary.box-shadow.dropdown-toggle(

From 40bb9c4721b45d3f036758ba178a6d5d34c4860a Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Jun 2022 14:31:59 -0400
Subject: [PATCH 031/110] Removed the remaining 'beta' labels.

---
 client/templates/includes/jstreeView.pug  | 4 ++--
 client/templates/pages/projectManager.pug | 2 +-
 client/views/jstree-view.js               | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/templates/includes/jstreeView.pug b/client/templates/includes/jstreeView.pug
index 64c3109a8f..e2f0075e83 100644
--- a/client/templates/includes/jstreeView.pug
+++ b/client/templates/includes/jstreeView.pug
@@ -23,8 +23,8 @@ div
       li.dropdown-item(id="fb-new-directory" data-hook="fb-new-directory") Create Directory
       li.dropdown-item(id="fb-new-project" data-hook="fb-new-project") Create Project
       li.dropdown-item(id="fb-new-model" data-hook="fb-new-model" data-type="model") Create Model
-      li.dropdown-item(id="fb-new-model" data-hook="fb-new-model" data-type="spatial") Create Spatial Model (beta)
-      li.dropdown-item(id="fb-new-model" data-hook="fb-new-domain") Create Domain (beta)
+      li.dropdown-item(id="fb-new-model" data-hook="fb-new-model" data-type="spatial") Create Spatial Model
+      li.dropdown-item(id="fb-new-model" data-hook="fb-new-domain") Create Domain
       li.dropdown-divider(data-hook="fb-proj-seperator")
       li.dropdown-item(id="fb-import-model" data-hook="fb-import-model") Add Existing Model
       li.dropdown-divider
diff --git a/client/templates/pages/projectManager.pug b/client/templates/pages/projectManager.pug
index 59bd4742bb..05476cf6c0 100644
--- a/client/templates/pages/projectManager.pug
+++ b/client/templates/pages/projectManager.pug
@@ -51,7 +51,7 @@ section.page
 
         ul.dropdown-menu(aria-labelledby="project-manager-add-model-btn")
           li.dropdown-item(id="new-model" data-hook="new-model" data-type="model") New Model
-          li.dropdown-item(id="new-model" data-hook="new-model" data-type="spatial") New Spatial Model (beta)
+          li.dropdown-item(id="new-model" data-hook="new-model" data-type="spatial") New Spatial Model
           li.dropdown-divider
           li.dropdown-item(id="existing-model" data-hook="existing-model") Existing Model
           li.dropdown-divider
diff --git a/client/views/jstree-view.js b/client/views/jstree-view.js
index 9c2c354584..529c7ebd87 100644
--- a/client/views/jstree-view.js
+++ b/client/views/jstree-view.js
@@ -597,7 +597,7 @@ module.exports = View.extend({
   },
   getNewDomainContext: function (node) {
     return this.buildContextBase({
-      label: "New Domain (beta)",
+      label: "New Domain",
       action: (data) => {
         this.createDomain(node.original._path);
       }
@@ -609,7 +609,7 @@ module.exports = View.extend({
       label: "New Model",
       submenu: {
         spatial: this.buildContextBase({
-          label: "Spatial (beta)",
+          label: "Spatial",
           action: (data) => {
             this.createModel(node, dirname, true, inProject);
           }

From 203830a799c824b3bb5e67cc866980c7b5a8189d Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 27 Jun 2022 15:34:42 -0400
Subject: [PATCH 032/110] Updated domain defaults.

---
 stochss_templates/nonSpatialModelTemplate.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss_templates/nonSpatialModelTemplate.json b/stochss_templates/nonSpatialModelTemplate.json
index b48bc4cbd9..ec682bfcf7 100644
--- a/stochss_templates/nonSpatialModelTemplate.json
+++ b/stochss_templates/nonSpatialModelTemplate.json
@@ -13,7 +13,7 @@
 		"size": null,
         "rho_0": 1.0,
         "c_0": 10,
-        "p_0": 10,
+        "p_0": 100.0,
         "gravity": [0, 0, 0],
         "x_lim": [0, 0],
         "y_lim": [0, 0],

From 7480b8994e895c4b8b5a59ac10f030c0965b09fa Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 28 Jun 2022 11:01:54 -0400
Subject: [PATCH 033/110] Added check to prevent errors when adding a new type
 and there are no existing particles.

---
 client/pages/domain-editor.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/pages/domain-editor.js b/client/pages/domain-editor.js
index 3c4d84e8a3..c85940e474 100644
--- a/client/pages/domain-editor.js
+++ b/client/pages/domain-editor.js
@@ -140,7 +140,9 @@ let DomainEditor = PageView.extend({
     let fixed = $(this.queryByHook("td-fixed")).prop("checked");
     if(this.selectedType === "new") {
       let name = this.domain.types.addType(vol, mass, nu, fixed)
-      this.addType(name);
+      if(this.domain.particles.length > 0) {
+        this.addType(name);
+      }
     }else{
       let type = this.domain.types.get(this.selectedType, "typeID")
       type.mass = mass;

From 2f40a19434364d1e4c9175554025dcc360bc13e6 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 5 Jul 2022 14:51:03 -0400
Subject: [PATCH 034/110] Removed unused files.

---
 client/templates/includes/meshEditor.pug | 13 -----
 client/views/mesh-editor.js              | 68 ------------------------
 client/views/view-initial-condition.js   | 35 ------------
 3 files changed, 116 deletions(-)
 delete mode 100644 client/templates/includes/meshEditor.pug
 delete mode 100644 client/views/mesh-editor.js
 delete mode 100644 client/views/view-initial-condition.js

diff --git a/client/templates/includes/meshEditor.pug b/client/templates/includes/meshEditor.pug
deleted file mode 100644
index 4b478b473a..0000000000
--- a/client/templates/includes/meshEditor.pug
+++ /dev/null
@@ -1,13 +0,0 @@
-div#mesh-editor.card.card-body
-
-  div
-
-    h3.inline Mesh Editor
-    button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-mesh", data-hook="collapse") -
-
-  div.collapse(class="show", id="collapse-mesh")
-
-    table.table
-      tbody
-        tr
-          td:  div(data-hook="num-subdomains-container")
\ No newline at end of file
diff --git a/client/views/mesh-editor.js b/client/views/mesh-editor.js
deleted file mode 100644
index 8d68926a04..0000000000
--- a/client/views/mesh-editor.js
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-var $ = require('jquery');
-//support files
-var app = require('../app');
-var tests = require('./tests');
-//views
-var View = require('ampersand-view');
-var InputView = require('./input');
-//templates
-var template = require('../templates/includes/meshEditor.pug');
-
-module.exports = View.extend({
-  template: template,
-  events: {
-    'change [data-hook=num-subdomains-container]' : 'updateSubdomains',
-    'click [data-hook=collapse]' : 'changeCollapseButtonText'
-  },
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-  },
-  render: function () {
-    View.prototype.render.apply(this, arguments);
-  },
-  update: function (e) {
-  },
-  updateValid: function () {
-  },
-  updateSubdomains: function () {
-    this.model.parent.trigger('mesh-update');
-  },
-  changeCollapseButtonText: function (e) {
-    app.changeCollapseButtonText(this, e);
-  },
-  subviews: {
-    inputSubdomains: {
-      hook: 'num-subdomains-container',
-      prepareView: function (el) {
-        return new InputView({
-          parent: this,
-          required: true,
-          name: 'numSubdomains',
-          label: 'Number of Subdomains',
-          test: tests.valueTests,
-          modelKey: 'count',
-          valueType: 'number',
-          value: this.model.count,
-        });
-      },
-    },
-  },
-});
\ No newline at end of file
diff --git a/client/views/view-initial-condition.js b/client/views/view-initial-condition.js
deleted file mode 100644
index 3709ebcd88..0000000000
--- a/client/views/view-initial-condition.js
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-//views
-var View = require('ampersand-view');
-//templates
-var template = require('../templates/includes/viewInitialCondition.pug');
-
-module.exports = View.extend({
-  template: template,
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-    let self = this;
-    this.types = [];
-    this.model.types.forEach(function (index) {
-      let type = self.model.collection.parent.domain.types.get(index, "typeID");
-      self.types.push(type.name)
-    });
-  },
-});
\ No newline at end of file

From 8edcfebba3365978e08594a79747c43c5228eaf0 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:25:58 -0400
Subject: [PATCH 035/110] Created a containerized domain view to reduce
 repeating code and organize views and templates.

---
 client/domain-view/domain-view.js             | 474 ++++++++++++++++++
 client/domain-view/domainView.pug             | 118 +++++
 .../templates/edit3DDomainView.pug            | 231 +++++++++
 .../templates/editParticleView.pug            |  83 +++
 client/domain-view/templates/editType.pug     |  96 ++++
 .../domain-view/templates/importMeshView.pug  | 137 +++++
 client/domain-view/templates/limitsView.pug   | 175 +++++++
 .../domain-view/templates/propertiesView.pug  | 123 +++++
 .../templates/typesDescriptionView.pug        |  36 ++
 client/domain-view/templates/typesView.pug    |  75 +++
 client/domain-view/templates/viewType.pug     |  38 ++
 .../domain-view/views/edit-3D-domain-view.js  | 302 +++++++++++
 client/domain-view/views/import-mesh-view.js  | 187 +++++++
 client/domain-view/views/limits-view.js       | 162 ++++++
 client/domain-view/views/particle-view.js     | 229 +++++++++
 client/domain-view/views/properties-view.js   | 176 +++++++
 client/domain-view/views/type-view.js         | 178 +++++++
 .../views/types-description-view.js           | 128 +++++
 client/domain-view/views/types-view.js        | 105 ++++
 19 files changed, 3053 insertions(+)
 create mode 100644 client/domain-view/domain-view.js
 create mode 100644 client/domain-view/domainView.pug
 create mode 100644 client/domain-view/templates/edit3DDomainView.pug
 create mode 100644 client/domain-view/templates/editParticleView.pug
 create mode 100644 client/domain-view/templates/editType.pug
 create mode 100644 client/domain-view/templates/importMeshView.pug
 create mode 100644 client/domain-view/templates/limitsView.pug
 create mode 100644 client/domain-view/templates/propertiesView.pug
 create mode 100644 client/domain-view/templates/typesDescriptionView.pug
 create mode 100644 client/domain-view/templates/typesView.pug
 create mode 100644 client/domain-view/templates/viewType.pug
 create mode 100644 client/domain-view/views/edit-3D-domain-view.js
 create mode 100644 client/domain-view/views/import-mesh-view.js
 create mode 100644 client/domain-view/views/limits-view.js
 create mode 100644 client/domain-view/views/particle-view.js
 create mode 100644 client/domain-view/views/properties-view.js
 create mode 100644 client/domain-view/views/type-view.js
 create mode 100644 client/domain-view/views/types-description-view.js
 create mode 100644 client/domain-view/views/types-view.js

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
new file mode 100644
index 0000000000..90d6743eba
--- /dev/null
+++ b/client/domain-view/domain-view.js
@@ -0,0 +1,474 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let path = require('path');
+let _ = require('underscore');
+//support files
+let app = require('../app');
+let Plotly = require('../lib/plotly');
+//models
+let Particle = require('../models/particle');
+//views
+let View = require('ampersand-view');
+let TypesView = require('./views/types-view');
+let LimitsView = require('./views/limits-view');
+let PropertiesView = require('./views/properties-view');
+let EditParticleView = require('./views/particle-view');
+let ImportMeshView = require('./views/import-mesh-view');
+let Edit3DDomainView = require('./views/edit-3D-domain-view');
+let TypesDescriptionView = require('./views/types-description-view');
+//templates
+let template = require('./domainView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'click [data-hook=collapse-domain-particles]' : 'changeCollapseButtonText',
+    'click [data-hook=add-new-particle]' : 'handleAddParticle',
+    'click [data-hook=save-selected-particle]' : 'handleSaveParticle',
+    'click [data-hook=remove-selected-particle]' : 'handleRemoveParticle',
+    'click [data-hook=collapse-domain-figure]' : 'changeCollapseButtonText'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.readOnly = attrs.readOnly ? attrs.readOnly : false;
+    this.elements = attrs.elements ? attrs.elements : null;
+    this.queryStr = attrs.queryStr;
+    this.newPart = this.createNewParticle();
+    this.actPart = {"part":null, "tn":0, "pn":0};
+    this.model.updateValid();
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    this.renderPropertiesView();
+    this.renderLimitsView();
+    this.renderTypesView();
+    if(!this.readOnly) {
+      this.renderNewParticleView();
+      this.renderEditParticleView();
+      this.renderTypesDescriptionView();
+      this.renderEdit3DDomainView();
+      this.renderImportMeshView();
+    }
+    if(!this.elements) {
+      this.elements = {
+        figure: this.queryByHook('domain-figure'),
+        figureEmpty: this.queryByHook('domain-figure-empty')
+      }
+    }
+    let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
+    app.getXHR(endpoint, {success: (err, response, body) => {
+      this.plot = body.fig;
+      this.traceTemp = body.trace_temp;
+      this.displayFigure();
+    }});
+  },
+  add3DDomain: function (limits, particles, plot) {
+    if(plot) {
+      this.plot = plot;
+    }
+    let limitsChanged = this.changeDomainLimits(limits, Boolean(plot));
+    particles.forEach((particle) => {
+      particle = new Particle(particle);
+      this.model.particles.addParticle({particle: particle});
+      this.addParticle({particle: particle});
+    });
+    if(limitsChanged) {
+      this.renderLimitsView();
+    }
+    this.renderTypesView();
+    this.resetFigure();
+  },
+  addMeshDomain: function (limits, particles, types, reset) {
+    let limitsChanged = this.changeDomainLimits(limits, reset);
+    if(types) {
+      this.addMissingTypes(types);
+    }
+    particles.forEach((particle) => {
+      particle = new Particle(particle);
+      this.model.particles.addParticle({particle: particle});
+      this.addParticle({particle: particle});
+    });
+    if(limitsChanged) {
+      this.renderLimitsView();
+    }
+    this.renderTypesView();
+    if(types) {
+      this.renderNewParticleView();
+      this.renderEditParticleView();
+      this.renderEdit3DDomainView();
+      this.renderImportMeshView();
+    }
+    this.resetFigure();
+  },
+  addMissingTypes: function (typeIDs) {
+    typeIDs.forEach((typeID) => {
+      if(!this.model.types.get(typeID, 'typeID')) {
+        let name = this.model.types.addType();
+        this.addType(name, {update: false});
+      }
+    });
+  },
+  addParticle: function ({particle=this.newPart}={}) {
+    this.plot.data[particle.type].ids.push(particle.particle_id);
+    this.plot.data[particle.type].x.push(particle.point[0]);
+    this.plot.data[particle.type].y.push(particle.point[1]);
+    this.plot.data[particle.type].z.push(particle.point[2]);
+  },
+  addType: function (name, {update=true}={}) {
+    let newTrace = JSON.parse(JSON.stringify(this.traceTemp));
+    newTrace.name = name;
+    this.plot.data.push(newTrace);
+    if(update) {
+      this.renderNewParticleView();
+      this.renderEditParticleView();
+      this.renderEdit3DDomainView();
+      this.renderImportMeshView();
+    }
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e)
+  },
+  changeDomainLimits: function (limits, reset) {
+    var limitsChanged = false;
+    if(reset) {
+      this.model.x_lim = limits.x_lim;
+      this.model.y_lim = limits.y_lim;
+      this.model.y_lim = limits.y_lim;
+      limitsChanged = true;
+    }else{
+      if(this.model.x_lim[0] > limits.x_lim[0]) {
+        this.model.x_lim[0] = limits.x_lim[0];
+        limitsChanged = true;
+      }
+      if(this.model.y_lim[0] > limits.y_lim[0]) {
+        this.model.y_lim[0] = limits.y_lim[0];
+        limitsChanged = true;
+      }
+      if(this.model.z_lim[0] > limits.z_lim[0]) {
+        this.model.z_lim[0] = limits.z_lim[0];
+        limitsChanged = true;
+      }
+      if(this.model.x_lim[1] < limits.x_lim[1]) {
+        this.model.x_lim[1] = limits.x_lim[1];
+        limitsChanged = true;
+      }
+      if(this.model.y_lim[1] < limits.y_lim[1]) {
+        this.model.y_lim[1] = limits.y_lim[1];
+        limitsChanged = true;
+      }
+      if(this.model.z_lim[1] < limits.z_lim[1]) {
+        this.model.z_lim[1] = limits.z_lim[1];
+        limitsChanged = true;
+      }
+    }
+    return limitsChanged;
+  },
+  changeParticleLocation: function () {
+    this.plot.data[this.actPart.tn].x[this.actPart.pn] = this.actPart.part.point[0];
+    this.plot.data[this.actPart.tn].y[this.actPart.pn] = this.actPart.part.point[1];
+    this.plot.data[this.actPart.tn].z[this.actPart.pn] = this.actPart.part.point[2];
+  },
+  changeParticleType: function (type, {update=true}={}) {
+    let id = this.plot.data[this.actPart.tn].ids.splice(this.actPart.pn, 1)[0];
+    let x = this.plot.data[this.actPart.tn].x.splice(this.actPart.pn, 1)[0];
+    let y = this.plot.data[this.actPart.tn].y.splice(this.actPart.pn, 1)[0];
+    let z = this.plot.data[this.actPart.tn].z.splice(this.actPart.pn, 1)[0];
+    this.plot.data[type].ids.push(id);
+    this.plot.data[type].x.push(x);
+    this.plot.data[type].y.push(y);
+    this.plot.data[type].z.push(z);
+    if(update) {
+      this.resetFigure();
+    }
+  },
+  createNewParticle: function () {
+    let type = this.model.types.get(0, 'typeID');
+    return new Particle({
+      c: type.c,
+      fixed: type.fixed,
+      mass: type.mass,
+      nu: type.nu,
+      point: [0, 0, 0],
+      rho: type.rho,
+      type: type.typeID,
+      volume: type.volume
+    });
+  },
+  completeAction: function (prefix) {
+    $(this.queryByHook(`${prefix}-in-progress`)).css("display", "none");
+    $(this.queryByHook(`${prefix}-complete`)).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook(`${prefix}-complete`)).css('display', 'none');
+    }, 5000);
+  },
+  deleteParticle: function () {
+    this.plot.data[this.actPart.tn].ids.splice(this.actPart.pn, 1);
+    this.plot.data[this.actPart.tn].x.splice(this.actPart.pn, 1);
+    this.plot.data[this.actPart.tn].y.splice(this.actPart.pn, 1);
+    this.plot.data[this.actPart.tn].z.splice(this.actPart.pn, 1);
+    this.resetFigure();
+  },
+  deleteType: function (type, {unassign=true}={}) {
+    if(unassign) {
+      this.unassignAllParticles(type, {update: false});
+    }else{
+      if(this.actPart.part && this.actPart.part.type === type) {
+        this.actPart = {"part":null, "tn":0, "pn":0};
+      }
+      if(this.newPart && this.newPart.type === type) {
+        this.newPart.type = 0
+      }
+      let particles = this.model.particles.filter((particle) => {
+        return particle.type === type;
+      });
+      this.model.particles.removeParticles(particles);
+    }
+    this.plot.data.splice(type, 1);
+    this.renderTypesView();
+    this.renderNewParticleView();
+    this.renderEditParticleView();
+    this.renderEdit3DDomainView();
+    this.renderImportMeshView();
+    this.resetFigure();
+  },
+  displayFigure: function () {
+    if(this.model.particles.length > 0) {
+      $(this.elements.figureEmpty).css('display', 'none');
+      $(this.elements.figure).css('display', 'block');
+      Plotly.newPlot(this.elements.figure, this.plot);
+      this.elements.figure.on('plotly_click', _.bind(this.selectParticle, this));
+    }else{
+      $(this.elements.figureEmpty).css('display', 'block');
+      $(this.elements.figure).css('display', 'none');
+    }
+  },
+  handleAddParticle: function () {
+    this.startAction("anp")
+    this.model.particles.addParticle({particle: this.newPart});
+    this.addParticle();
+    this.resetFigure();
+    this.renderTypesView();
+    this.newPart = this.createNewParticle();
+    this.renderNewParticleView();
+    this.completeAction("anp");
+  },
+  handleRemoveParticle: function () {
+    this.startAction("rsp")
+    this.model.particles.removeParticle(this.actPart.part);
+    this.deleteParticle();
+    this.actPart = {"part":null, "tn":0, "pn":0};
+    this.renderTypesView();
+    this.renderEditParticleView();
+    this.completeAction("rsp")
+  },
+  handleSaveParticle: function () {
+    this.startAction("esp");
+    if(this.editParticleView.origType !== this.actPart.part.type) {
+      this.changeParticleType(this.actPart.part.type, {update: false});
+      this.renderTypesView();
+    }
+    if(!this.actPart.part.comparePoint(this.editParticleView.origPoint)) {
+      this.changeParticleLocation();
+    }
+    this.resetFigure();
+    this.completeAction("esp");
+  },
+  removeFigure: function () {
+    try {
+      this.elements.figure.removeListener('plotly_click', this.selectParticle);
+      Plotly.purge(this.elements.figure);
+    }catch (err) {
+      return
+    }
+  },
+  renameType: function (index, name) {
+    this.plot.data[index].name = name;
+    this.renderNewParticleView();
+    this.renderEditParticleView();
+    this.renderEdit3DDomainView();
+    this.renderImportMeshView();
+    this.resetFigure();
+  },
+  renderEdit3DDomainView: function () {
+    if(this.edit3DDomainView) {
+      this.edit3DDomainView.remove();
+    }
+    this.edit3DDomainView = new Edit3DDomainView();
+    app.registerRenderSubview(this, this.edit3DDomainView, "3d-domain-container");
+  },
+  renderEditParticleView: function () {
+    if(this.editParticleView) {
+      this.editParticleView.remove();
+    }
+    let disable = this.actPart.part == null
+    this.editParticleView = new EditParticleView({
+      model: this.actPart.part ? this.actPart.part : this.createNewParticle(),
+      defaultType: this.model.types.get(this.actPart.part ? this.actPart.part.type : 0, "typeID"),
+      viewIndex: 1,
+      disable: disable
+    });
+    app.registerRenderSubview(this, this.editParticleView, "edit-particle-container");
+    $(this.queryByHook("edit-select-message")).css('display', disable ? 'block' : 'none');
+    $(this.queryByHook("save-selected-particle")).prop('disabled', disable);
+    $(this.queryByHook("remove-selected-particle")).prop('disabled', disable);
+  },
+  renderImportMeshView: function () {
+    if(this.importMeshView) {
+      this.importMeshView.remove();
+    }
+    this.importMeshView = new ImportMeshView();
+    app.registerRenderSubview(this, this.importMeshView, "import-particles-section");
+  },
+  renderLimitsView: function () {
+    if(this.limitsView) {
+      this.limitsView.remove();
+    }
+    this.limitsView = new LimitsView({
+      model: this.model,
+      readOnly: this.readOnly
+    });
+    app.registerRenderSubview(this, this.limitsView, "domain-limits-container");
+  },
+  renderNewParticleView: function () {
+    if(this.newParticleView) {
+      this.newParticleView.remove();
+    }
+    this.newParticleView = new EditParticleView({
+      model: this.newPart,
+      defaultType: this.model.types.get(0, "typeID"),
+      viewIndex: 0
+    });
+    app.registerRenderSubview(this, this.newParticleView, "new-particle-container");
+  },
+  renderPropertiesView: function () {
+    if(this.propertiesView) {
+      this.propertiesView.remove();
+    }
+    this.propertiesView = new PropertiesView({
+      model: this.model,
+      readOnly: this.readOnly
+    });
+    app.registerRenderSubview(this, this.propertiesView, "domain-properties-container");
+  },
+  renderTypesDescriptionView: function () {
+    if(this.typesDescriptionView) {
+      this.typesDescriptionView.remove();
+    }
+    this.typesDescriptionView = new TypesDescriptionView();
+    app.registerRenderSubview(this, this.typesDescriptionView, "particle-types-container");
+  },
+  renderTypesView: function () {
+    if(this.typesView) {
+      this.typesView.remove();
+    }
+    let particleCounts = {};
+    this.model.particles.forEach((particle) => {
+      if(particleCounts[particle.type]) {
+        particleCounts[particle.type] += 1;
+      }else{
+        particleCounts[particle.type] = 1;
+      }
+    });
+    this.model.types.forEach((dType) => {
+      if(particleCounts[dType.typeID]) {
+        dType.numParticles = particleCounts[dType.typeID];
+      }else{
+        dType.numParticles = 0;
+      }
+    });
+    this.typesView = new TypesView({
+      collection: this.model.types,
+      readOnly: this.readOnly
+    });
+    app.registerRenderSubview(this, this.typesView, "domain-types-container");
+  },
+  resetFigure: function () {
+    this.removeFigure();
+    this.displayFigure();
+  },
+  selectParticle: function (data) {
+    let point = data.points[0];
+    this.actPart.part = this.model.particles.get(point.id, 'particle_id');
+    this.actPart.tn = point.curveNumber;
+    this.actPart.pn = point.pointNumber;
+    this.renderEditParticleView();
+  },
+  setParticleTypes: function (typeIDs, types) {
+    this.addMissingTypes(typeIDs);
+    let actPart = JSON.parse(JSON.stringify(this.actPart));
+    types.forEach((type) => {
+      let particle = this.model.particles.get(type.particle_id, 'particle_id');
+      this.actPart = {
+        part: particle,
+        tn: particle.type,
+        pn: this.plot.data[particle.type].ids.indexOf(particle.particle_id)
+      }
+      this.changeParticleType(type.typeID, {update: false});
+      particle.type = type.typeID;
+    });
+    if(actPart.part && actPart.part.type === type) {
+      this.actPart = {
+        part: this.model.particles.get(actPart.part.particle_id, "particle_id"),
+        tn: 0,
+        pn: this.plot.data[0].ids.indexOf(actPart.part.particle_id)
+      }
+      this.renderEditParticleView();
+    }else{
+      this.actPart = actPart
+    }
+    this.resetFigure();
+    this.renderNewParticleView();
+    this.renderEditParticleView();
+    this.renderEdit3DDomainView();
+    this.renderImportMeshView();
+  },
+  startAction: function (prefix) {
+    $(this.queryByHook(`${prefix}-complete`)).css('display', 'none');
+    $(this.queryByHook(`${prefix}-in-progress`)).css("display", "inline-block");
+  },
+  unassignAllParticles: function (type, {update=true}={}) {
+    let actPart = JSON.parse(JSON.stringify(this.actPart));
+    this.model.particles.forEach((particle) => {
+      if(particle.type === type) {
+        this.actPart = {
+          part: particle,
+          tn: type,
+          pn: this.plot.data[type].ids.indexOf(particle.particle_id)
+        }
+        this.changeParticleType(0, {update: false});
+        particle.type = 0;
+      }
+    });
+    if(actPart.part && actPart.part.type === type) {
+      this.actPart = {
+        part: this.model.particles.get(actPart.part.particle_id, "particle_id"),
+        tn: 0,
+        pn: this.plot.data[0].ids.indexOf(actPart.part.particle_id)
+      }
+      this.renderEditParticleView();
+    }else{
+      this.actPart = actPart
+    }
+    if(update) {
+      this.renderTypesView();
+      this.resetFigure();
+    }
+  }
+});
diff --git a/client/domain-view/domainView.pug b/client/domain-view/domainView.pug
new file mode 100644
index 0000000000..6ca9c7a9ab
--- /dev/null
+++ b/client/domain-view/domainView.pug
@@ -0,0 +1,118 @@
+div#domain-view
+
+  div(data-hook="domain-properties-container")
+
+  div(data-hook="domain-limits-container")
+
+  div(data-hook="domain-types-container")
+
+  div#domain-particles-editor.card
+
+    div.card-header.pb-0
+
+      h3.inline.mr-3 Particles
+
+      div.inline.mr-3
+
+        ul.nav.nav-tabs.card-header-tabs(id="domain-particles-tabs")
+
+          li.nav-item
+
+            a.nav-link.tab.active(data-hook="new-particle-tab" data-toggle="tab" href="#create-new-particle") Create New
+
+          li.nav-item
+
+            a.nav-link.tab(data-hook="edit-particle-tab" data-toggle="tab" href="#edit-selected-particle") Edit Selected
+
+          li.nav-item
+
+            a.nav-link.tab(data-hook="particle-types-tab" data-toggle="tab" href="#set-particle-types") Set Particle Types
+
+          li.nav-item
+
+            a.nav-link.tab(data-hook="3d-domain-tab" data-toggle="tab" href="#create-3d-domain") Create 3D Domain
+
+          li.nav-item
+
+            a.nav-link.tab(data-hook="import-particles-tab" data-toggle="tab" href="#import-particles") Import Mesh
+
+      button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#domain-particles-section" data-hook="collapse-domain-particles") -
+
+    div.collapse.show(id="domain-particles-section" data-hook="domain-particles-section")
+
+      div.card-body.tab-content
+
+        div.tab-pane.active(id="create-new-particle" data-hook="new-particle-section")
+
+          div(data-hook="new-particle-container")
+
+          button.btn.btn-outline-primary.box-shadow(data-hook="add-new-particle") Add Particle
+
+          div.mdl-edit-btn.saving-status.inline(data-hook="anp-in-progress")
+
+            div.spinner-grow.mr-2
+
+            span Adding particle ...
+
+          div.mdl-edit-btn.saved-status.inline(data-hook="anp-complete")
+
+            span Particle Added
+
+        div.tab-pane(id="edit-selected-particle" data-hook="edit-particle-section")
+
+          div.text-info.mb-4(data-hook="edit-select-message" style="display: none")
+            | Click on a particle in the Domain section to begin editing.
+
+          div(data-hook="edit-particle-container")
+
+          button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="save-selected-particle") Save Particle
+
+          div.mdl-edit-btn.saving-status.inline(data-hook="esp-in-progress")
+
+            div.spinner-grow.mr-2
+
+            span Saving particle ...
+
+          div.mdl-edit-btn.saved-status.inline(data-hook="esp-complete")
+
+            span Particle Saved
+
+          button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="remove-selected-particle") Remove Particle
+
+          div.mdl-edit-btn.saving-status.inline(data-hook="rsp-in-progress")
+
+            div.spinner-grow.mr-2
+
+            span Removing particle ...
+
+          div.mdl-edit-btn.saved-status.inline(data-hook="rsp-complete")
+
+            span Particle Removed
+
+        div.tab-pane(id="set-particle-types" data-hook="set-particle-types-section")
+
+          div(data-hook="particle-types-container")
+
+        div.tab-pane(id="create-3d-domain" data-hook="3d-domain-section")
+
+          div(data-hook="3d-domain-container")
+
+        div.tab-pane(id="import-particles" data-hook="import-particles-section")
+
+          div(data-hook="import-particles-container")
+
+  div#domain-figure-preview.card
+
+    div.card-header.pb-0
+
+      h3.inline.mr-3 Domain
+
+      button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#domain-figure-container" data-hook="collapse-domain-figure") -
+
+    div.collapse.show(id="domain-figure-container" data-hook="domain-figure-container")
+
+      div.card-body
+
+        div(id="domain-figure" data-hook="domain-figure" style="height: 800px")
+
+        div.text-danger(data-hook="domain-figure-empty") The domain currently has no particles to display
\ No newline at end of file
diff --git a/client/domain-view/templates/edit3DDomainView.pug b/client/domain-view/templates/edit3DDomainView.pug
new file mode 100644
index 0000000000..7e3a60dd29
--- /dev/null
+++ b/client/domain-view/templates/edit3DDomainView.pug
@@ -0,0 +1,231 @@
+div.mx-1
+
+  h4.mt-3 Particle Distribution
+
+  div
+
+    hr
+
+    div.mb-3.mx-1.row.head.align-items-baseline
+
+      div.col-sm-3
+
+      div.col-sm-2
+
+        h6.inline <b>X-Plane</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Y-Plane</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Z-Plane</b>
+
+      div.col-sm-3
+
+        h6.inline <b>Total</b>
+
+    div.row
+
+      div.col-sm-3
+
+        h6.inline <b>Number of Particles</b>
+
+      div.col-sm-2
+
+        div(data-target="edit-3d-domain-n" data-hook="edit-3d-domain-nx" data-key="nx")
+
+      div.col-sm-2
+
+        div(data-target="edit-3d-domain-n" data-hook="edit-3d-domain-ny" data-key="ny")
+
+      div.col-sm-2
+
+        div(data-target="edit-3d-domain-n" data-hook="edit-3d-domain-nz" data-key="nz")
+
+      div.col-sm-3
+
+        div(data-target="3d-domain-n" data-hook="3d-domain-n")
+
+  h4.mt-3 Domain Limits
+
+  div
+
+    div.mx-1.row.head.align-items-baseline
+
+      div.col-sm-3
+      
+      div.col-sm-3
+
+        h6.inline <b>X-Axis</b>
+
+      div.col-sm-3
+
+        h6.inline <b>Y-Axis</b>
+
+      div.col-sm-3
+
+        h6.inline <b>Z-Axis</b>
+
+    div.mt-3.mx-1.row
+
+      div.col-sm-3
+
+        h6.inline <b>Minimum</b>
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-x-lim-min" data-target="edit-3d-domain-limitation" data-name="xLim" data-index="0")
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-y-lim-min" data-target="edit-3d-domain-limitation" data-name="yLim" data-index="0")
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-z-lim-min" data-target="edit-3d-domain-limitation" data-name="zLim" data-index="0")
+
+    hr
+
+    div.mx-1.row
+
+      div.col-sm-3
+
+        h6.inline <b>Maximum</b>
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-x-lim-max" data-target="edit-3d-domain-limitation" data-name="xLim" data-index="1")
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-y-lim-max" data-target="edit-3d-domain-limitation" data-name="yLim" data-index="1")
+
+      div.col-sm-3
+
+        div(data-hook="edit-3d-domain-z-lim-max" data-target="edit-3d-domain-limitation" data-name="zLim" data-index="1")
+
+  div.mt-3
+
+    h4.inline Advanced
+
+    button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#edit-3D-domain-advanced" data-hook="collapse-3D-domain-advanced") +
+
+  div.collapse(id="edit-3D-domain-advanced" data-hook="3D-domain-advanced-container")
+
+    div.mt-3
+
+      h5.inline.mr-2 Type:
+
+      div.inline(data-hook="edit-3d-domain-type-select")
+
+    div.mt-3
+
+      h5 Type Defaults
+
+      hr
+
+      div.mb-3.mx-1.row.head.align-items-baseline
+
+        div.col-sm-2
+
+          h6.inline <b>Mass</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Volume</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Density</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Viscosity</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Speed of Sound</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Fixed</b>
+
+      div.row.pl-3
+
+        div.col-sm-2
+
+          div(data-hook="edit-3d-domain-td-mass")
+
+        div.col-sm-2
+
+          div(data-hook="edit-3d-domain-td-vol")
+
+        div.col-sm-2
+
+          div(data-hook="edit-3d-domain-td-rho")
+
+        div.col-sm-2
+
+          div(data-hook="edit-3d-domain-td-nu")
+
+        div.col-sm-2
+
+          div(data-hook="edit-3d-domain-td-c")
+
+        div.col-sm-2
+
+          input(type="checkbox" data-hook="edit-3d-domain-td-fixed" disabled)
+
+    div.my-3
+
+      h5 Particle Transformations
+
+      hr
+
+      div.mb-3.mx-1.row.head.align-items-baseline
+
+        div.col-sm-4
+
+          h6.inline <b>X-Axis</b>
+
+        div.col-sm-4
+
+          h6.inline <b>Y-Axis</b>
+
+        div.col-sm-4
+
+          h6.inline <b>Z-Axis</b>
+
+      div.row
+
+        div.col-sm-4
+
+          div(data-target="edit-3d-domain-trans" data-hook="edit-3d-domain-x-trans" data-index="0")
+
+        div.col-sm-4
+
+          div(data-target="edit-3d-domain-trans" data-hook="edit-3d-domain-y-trans" data-index="1")
+
+        div.col-sm-4
+
+          div(data-target="edit-3d-domain-trans" data-hook="edit-3d-domain-z-trans" data-index="2")
+
+  div.inline
+
+    button.btn.btn-outline-primary(data-hook="build-3d-domain") Build Domain
+
+  div.mdl-edit-btn.saving-status.inline(data-hook="c3dd-in-progress")
+
+    div.spinner-grow.mr-2
+
+    span Creating domain ...
+
+  div.mdl-edit-btn.saved-status.inline(data-hook="c3dd-complete")
+
+    span Domain successfully created
+
+  div.mdl-edit-btn.save-error-status(data-hook="c3dd-error")
+
+    span(data-hook="c3dd-action-error")
diff --git a/client/domain-view/templates/editParticleView.pug b/client/domain-view/templates/editParticleView.pug
new file mode 100644
index 0000000000..0ab7f02d4e
--- /dev/null
+++ b/client/domain-view/templates/editParticleView.pug
@@ -0,0 +1,83 @@
+div.mx-1
+
+  div
+
+    h4.inline.mr-2 Type:
+
+    div.inline(data-target="type" data-hook=`particle-type-${this.viewIndex}`)
+
+  div
+
+    h4.inline.mr-2 Location:
+
+    div.inline.mr-2 (x:
+
+    div.inline.ml2(data-target=`location-${this.viewIndex}` data-hook=`x-coord-${this.viewIndex}` data-index="0")
+
+    div.inline.mr-2 ,  y:
+
+    div.inline.ml2(data-target=`location-${this.viewIndex}` data-hook=`y-coord-${this.viewIndex}` data-index="1")
+
+    div.inline.mr-2 ,  z:
+
+    div.inline.ml2(data-target=`location-${this.viewIndex}` data-hook=`z-coord-${this.viewIndex}` data-index="2")
+
+    div.inline )
+
+  h4 Particle Properties
+
+  div.pl-2(data-hook="particle-details")
+
+    hr
+
+    div.mb-3.mx-1.row.head.align-items-baseline
+
+      div.col-sm-2
+
+        h6.inline <b>Mass</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Volume<b>
+
+      div.col-sm-2
+
+        h6.inline <b>Density</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Viscosity</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Speed of Sound</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Fixed</b>
+
+    div.row
+
+      div.col-sm-2
+
+        div(data-hook=`particle-mass-${this.viewIndex}`)
+
+      div.col-sm-2
+
+        div(data-hook=`particle-vol-${this.viewIndex}`)
+
+      div.col-sm-2
+
+        div(data-hook=`particle-rho-${this.viewIndex}`)
+
+      div.col-sm-2
+
+        div(data-hook=`particle-nu-${this.viewIndex}`)
+
+      div.col-sm-2
+
+        div(data-hook=`particle-c-${this.viewIndex}`)
+
+      div.col-sm-2
+
+        input(type="checkbox" data-hook=`particle-fixed-${this.viewIndex}`)
\ No newline at end of file
diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
new file mode 100644
index 0000000000..5316ee01e5
--- /dev/null
+++ b/client/domain-view/templates/editType.pug
@@ -0,0 +1,96 @@
+div.mx-1
+
+  if(this.model.collection.indexOf(this.model) !== 1)
+    hr
+
+  div.row
+
+    div.col-sm-1
+
+      div.pl-3
+
+        input(type="checkbox" data-hook="select" data-toggle="collapse" data-target="#collapse-type-details" + this.model.typeID)
+
+    div.col-sm-3
+
+      div(data-hook="type-name" data-target=this.model.typeID)
+
+    div.col-sm-3
+
+      div=this.model.numParticles
+
+    div.col-sm-3
+
+      button.btn.btn-outline-secondary.box-shadow(data-type=this.model.typeID data-hook='unassign-all') Un-Assign Particles
+
+    div.col-sm-2
+
+      button.btn.btn-outline-secondary.box-shadow.dropdown-toggle(
+        id="delete-domain-type",
+        data-toggle="dropdown",
+        aria-haspopup="true",
+        aria-expanded="false",
+        type="button"
+      ) Delete <span class="caret"></span>
+
+      ul.dropdown-menu(aria-labelledby="delete-domain-type")
+        li.dropdown-item(data-hook="delete-type" data-type=this.model.typeID) Type
+        li.dropdown-item(data-hook="delete-all" data-type=this.model.typeID) Type and Particles
+
+  div-mx-1.pl-2(data-hook="type-details")
+
+    div.collapse(id="collapse-type-details" + this.model.typeID)
+
+      hr
+
+      div.mb-3.mx-1.row.head.align-items-baseline
+
+        div.col-sm-2
+
+          h6.inline <b>Mass</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Volume</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Density</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Viscosity</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Speed of Sound</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Fixed</b>
+
+      div.row
+
+        div.col-sm-2
+
+          div(data-hook="td-mass" data-target="type-defaults")
+
+        div.col-sm-2
+
+          div(data-hook="td-vol" data-target="type-defaults")
+
+        div.col-sm-2
+
+          div(data-hook="td-rho" data-target="type-defaults")
+
+        div.col-sm-2
+
+          div(data-hook="td-nu" data-target="type-defaults")
+
+        div.col-sm-2
+
+          div(data-hook="td-c" data-target="type-defaults")
+
+        div.col-sm-2
+
+          input(type="checkbox" data-hook="td-fixed")
\ No newline at end of file
diff --git a/client/domain-view/templates/importMeshView.pug b/client/domain-view/templates/importMeshView.pug
new file mode 100644
index 0000000000..000a38acc3
--- /dev/null
+++ b/client/domain-view/templates/importMeshView.pug
@@ -0,0 +1,137 @@
+div.mx-1
+
+  div.my-3
+
+    span.inline.mr-2(for="meshfile") Please specify a mesh to import: 
+
+    input(id="meshfile" type="file" name="meshfile" size="30" accept=".xml" required)
+
+  div.mb-3
+
+    span.inline.mr-2(for=typefile) Type descriptions (optional):
+
+    input(id="typefile" type="file" name="typefile" size="30" accept=".txt")
+
+  div.mt-3
+
+    h4.inline Advanced
+
+    button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#import-mesh-advanced" data-hook="collapse-import-mesh-advanced") +
+
+  div.collapse(id="import-mesh-advanced" data-hook="import-mesh-container")
+
+    div.mt-3
+
+      h5.inline.mr-2 Type:
+
+      div.inline(data-hook="import-mesh-type-select")
+
+    div.mt-3
+
+      h5 Type Defaults
+
+      hr
+
+      div.mb-3.mx-1.row.head.align-items-baseline
+
+        div.col-sm-2
+
+          h6.inline <b>Mass</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Volume</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Density</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Viscosity</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Speed of Sound</b>
+
+        div.col-sm-2
+
+          h6.inline <b>Fixed</b>
+
+      div.row.pl-3
+
+        div.col-sm-2
+
+          div(data-hook="import-mesh-td-mass")
+
+        div.col-sm-2
+
+          div(data-hook="import-mesh-td-vol")
+
+        div.col-sm-2
+
+          div(data-hook="import-mesh-td-rho")
+
+        div.col-sm-2
+
+          div(data-hook="import-mesh-td-nu")
+
+        div.col-sm-2
+
+          div(data-hook="import-mesh-td-c")
+
+        div.col-sm-2
+
+          input(type="checkbox" data-hook="import-mesh-td-fixed" disabled)
+
+    div.my-3
+
+      h5 Particle Transformations
+
+      hr
+
+      div.mb-3.mx-1.row.head.align-items-baseline
+
+        div.col-sm-4
+
+          h6.inline <b>X-Axis</b>
+
+        div.col-sm-4
+
+          h6.inline <b>Y-Axis</b>
+
+        div.col-sm-4
+
+          h6.inline <b>Z-Axis</b>
+
+      div.row
+
+        div.col-sm-4
+
+          div(data-target="import-mesh-trans" data-hook="import-mesh-x-trans" data-index="0")
+
+        div.col-sm-4
+
+          div(data-target="import-mesh-trans" data-hook="import-mesh-y-trans" data-index="1")
+
+        div.col-sm-4
+
+          div(data-target="import-mesh-trans" data-hook="import-mesh-z-trans" data-index="2")
+
+  div.inline
+
+    button.btn.btn-outline-primary.box-shadow(data-hook="import-mesh-particles" disabled) Import Mesh
+
+  div.mdl-edit-btn.saving-status.inline(data-hook="imp-in-progress")
+
+    div.spinner-grow.mr-2
+
+    span Importing mesh ...
+
+  div.mdl-edit-btn.saved-status.inline(data-hook="imp-complete")
+
+    span
+
+  div.mdl-edit-btn.save-error-status(data-hook="imp-error")
+
+    span(data-hook="imp-action-error")
\ No newline at end of file
diff --git a/client/domain-view/templates/limitsView.pug b/client/domain-view/templates/limitsView.pug
new file mode 100644
index 0000000000..6c13b2af23
--- /dev/null
+++ b/client/domain-view/templates/limitsView.pug
@@ -0,0 +1,175 @@
+div#domain-limits-editor.card
+
+  div.card-header.pb-0
+
+    h3.inline.mr-3 Limits
+
+    div.inline.mr-3
+
+      ul.nav.nav-tabs.card-header-tabs(id="domain-limits-tabs")
+
+        li.nav-item
+
+          a.nav-link.tab.active(data-hook="domain-limits-edit-tab" data-toggle="tab" href="#edit-domain-limits") Edit
+
+        li.nav-item
+
+          a.nav-link.tab(data-hook="domain-limits-view-tab" data-toggle="tab" href="#view-domain-limits") View
+
+    button.btn.btn-ouline-collapse(data-toggle="collapse" data-target="#domain-limits-section" data-hook="collapse-domain-limits") -
+
+  div.collapse.show(id="domain-limits-section" data-hook="domain-limits-section")
+
+    div.card-body.tab-content
+
+      div.tab-pane.active(id="edit-domain-limits" data-hook="edit-domnain-limits")
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-3
+          
+          div.col-sm-3
+
+            h6.inline <b>X-Axis</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Y-Axis</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Z-Axis</b>
+
+        div.mt-3.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Minimum</b>
+
+          div.col-sm-3
+
+            div(data-hook="x-lim-min" data-target="limitation" data-name="x_lim" data-index="0")
+
+          div.col-sm-3
+
+            div(data-hook="y-lim-min" data-target="limitation" data-name="y_lim" data-index="0")
+
+          div.col-sm-3
+
+            div(data-hook="z-lim-min" data-target="limitation" data-name="z_lim" data-index="0")
+
+        hr
+
+        div.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Maximum</b>
+
+          div.col-sm-3
+
+            div(data-hook="x-lim-max" data-target="limitation" data-name="x_lim" data-index="1")
+
+          div.col-sm-3
+
+            div(data-hook="y-lim-max" data-target="limitation" data-name="y_lim" data-index="1")
+
+          div.col-sm-3
+
+            div(data-hook="z-lim-max" data-target="limitation" data-name="z_lim" data-index="1")
+
+        hr
+
+        div.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Reflect</b>
+
+          div.col-sm-3
+
+            input(type="checkbox" id="x-reflect" data-hook="reflect_x" data-target="reflect" disabled)
+
+          div.col-sm-3
+
+            input(type="checkbox" id="y-reflect" data-hook="reflect_y" data-target="reflect" disabled)
+
+          div.col-sm-3
+
+            input(type="checkbox" id="z-reflect" data-hook="reflect_z" data-target="reflect" disabled)
+
+      div.tab-pane(id="view-domain-limits" data-hook="view-domain-limits")
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-3
+          
+          div.col-sm-3
+
+            h6.inline <b>X-Axis</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Y-Axis</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Z-Axis</b>
+
+        div.mt-3.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Minimum</b>
+
+          div.col-sm-3
+
+            div=this.model.x_lim[0]
+
+          div.col-sm-3
+
+            div=this.model.y_lim[0]
+
+          div.col-sm-3
+
+            div=this.model.z_lim[0]
+
+        hr
+
+        div.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Maximum</b>
+
+          div.col-sm-3
+
+            div=this.model.x_lim[1]
+
+          div.col-sm-3
+
+            div=this.model.y_lim[1]
+
+          div.col-sm-3
+
+            div=this.model.z_lim[1]
+
+        hr
+
+        div.mx-1.row
+
+          div.col-sm-3
+
+            h6.inline <b>Reflect</b>
+
+          div.col-sm-3
+
+            input(type="checkbox" id="x-reflect" data-hook="view-reflect_x" data-target="reflect" disabled)
+
+          div.col-sm-3
+
+            input(type="checkbox" id="y-reflect" data-hook="view-reflect_y" data-target="reflect" disabled)
+
+          div.col-sm-3
+
+            input(type="checkbox" id="z-reflect" data-hook="view-reflect_z" data-target="reflect" disabled)
\ No newline at end of file
diff --git a/client/domain-view/templates/propertiesView.pug b/client/domain-view/templates/propertiesView.pug
new file mode 100644
index 0000000000..b6bc871a94
--- /dev/null
+++ b/client/domain-view/templates/propertiesView.pug
@@ -0,0 +1,123 @@
+div#domain-properties-editor.card
+
+  div.card-header.pb-0
+    
+    h3.inline.mr-3 Properties
+
+    div.inline.mr-3
+
+      ul.nav.nav-tabs.card-header-tabs(id="domain-properties-tabs")
+
+        li.nav-item
+
+          a.nav-link.tab.active(data-hook="domain-properties-edit-tab" data-toggle="tab" href="#edit-domain-properties") Edit
+
+        li.nav-item
+
+          a.nav-link.tab(data-hook="domain-properties-view-tab" data-toggle="tab" href="#view-domain-properties") View
+
+    button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#domain-properties-section" data-hook="collapse-domain-properties") -
+
+  div.collapse.show(id="domain-properties-section" data-hook="domain-properties-section")
+
+    div.card-body.tab-content
+
+      div.tab-pane.active(id="edit-domain-properties" data-hook="edit-domain-properties")
+        
+        div
+
+          span.mr-3(for="#static-domain") <b>Static Domain</b>:
+
+          input(type="checkbox" id="static-domain" data-hook="static-domain")
+
+        hr
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-3
+
+            h6.inline <b>Density</b>
+            
+          div.col-sm-3
+
+            h6.inline <b>Gravity</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Pressure</b>
+
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.pressure) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+          div.col-sm-3
+
+            h6.inline <b>Speed of Sound</b>
+
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.speed) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
+        div.mt-3.mx-1.row
+
+          div.col-sm-3
+
+            div(data-hook="density")
+
+          div.col-sm-3
+
+            div(data-target="gravity" data-hook="gravity-x" data-index="0")
+            
+            div(data-target="gravity" data-hook="gravity-y" data-index="1")
+            
+            div(data-target="gravity" data-hook="gravity-z" data-index="2")
+
+          div.col-sm-3
+
+            div(data-hook="pressure")
+
+          div.col-sm-3
+
+            div(data-hook="speed")
+
+      div.tab-pane(id="view-domain-properties" data-hook="view-domain-properties")
+
+        div
+
+          span.mr-3(for="#view-static-domain") <b>Static Domain</b>:
+
+          input(type="checkbox" id="view-static-domain" data-hook="view-static-domain" disabled)
+
+        hr
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-3
+
+            h6.inline <b>Density</b>
+            
+          div.col-sm-3
+
+            h6.inline <b>Gravity</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Pressure</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Speed of Sound</b>
+
+        div.mt-3.mx-1.row
+
+          div.col-sm-3
+
+            div=this.model.rho_0
+
+          div.col-sm-3
+
+            div=`(X: ${this.model.gravity[0]}, Y: ${this.model.gravity[1]}, Z: ${this.model.gravity[2]})`
+
+          div.col-sm-3
+
+            div=this.model.p_0
+
+          div.col-sm-3
+
+            div=this.model.c_0
\ No newline at end of file
diff --git a/client/domain-view/templates/typesDescriptionView.pug b/client/domain-view/templates/typesDescriptionView.pug
new file mode 100644
index 0000000000..f4f2ab190e
--- /dev/null
+++ b/client/domain-view/templates/typesDescriptionView.pug
@@ -0,0 +1,36 @@
+div.mx-1
+
+  div.text-info(data-hook="type-location-message" style="display: none")
+    | There are multiple type files with that name, please select a location
+
+  div
+
+    div.inline.mr-3
+
+      span.inline.mr-2(for="file-select") Select type description file:
+
+      div.inline(id="file-select" data-hook="file-select")
+
+    div.inline(data-hook="file-location-container" style="display: none")
+
+      span.inlinemr-2(for="file-location-select") Location:
+
+      div.inline(id="file-location-select" data-hook="file-location-select")
+
+  div.my-3
+
+    button.btn.btn-outline-primary.box-shadow(data-hook="set-particle-types-btn" disabled) Set Types
+
+    div.mdl-edit-btn.saving-status.inline(data-hook="st-in-progress")
+
+      div.spinner-grow.mr-2
+
+      span Setting types ...
+
+    div.mdl-edit-btn.saved-status.inline(data-hook="st-complete")
+
+      span
+
+    div.mdl-edit-btn.save-error-status(data-hook="st-error")
+
+      span(data-hook="st-error-action")
\ No newline at end of file
diff --git a/client/domain-view/templates/typesView.pug b/client/domain-view/templates/typesView.pug
new file mode 100644
index 0000000000..d51f270214
--- /dev/null
+++ b/client/domain-view/templates/typesView.pug
@@ -0,0 +1,75 @@
+div#domain-types-editor.card
+
+  div.card-header.pb-0
+
+    h3.inline.mr-3 Types
+
+    div.inline.mr-3
+
+      ul.nav.nav-tabs.card-header-tabs(id="domain-types-teabs")
+
+        li.nav-item
+
+          a.nav-link.tab.active(data-hook="domain-types-edit-tab" data-toggle="tab" href="#edit-domain-types") Edit
+
+        li.nav-item
+
+          a.nav-link.tab(data-hook="domain-types-view-tab" data-toggle="tab" href="#view-domain-types") View
+
+    button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#domain-types-section" data-hook="collapse-domain-types") -
+
+  div.collapse.show(id="domain-types-section" data-hook="domain-types-section")
+
+    div.card-body.tab-content
+
+      div
+
+        span.mr-3.inline(for="unassigned-type-count") Number of Un-Assigned Particles: 
+
+        div.inline(id="unassigned-type-count" data-hook="unassigned-type-count")=this.collection.models[0].numParticles
+
+        div(data-hook="domain-error")
+
+          p.text-danger A domain cannot have any un-assigned particles.
+
+      div.tab-pane.active(id="edit-domain-types" data-hook="edit-domain-types")
+
+        hr
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-1
+
+            h6.inline <b>Edit</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Name</b>
+
+          div.col-sm-8
+
+            h6.inline <b>Number of Particles</b>
+
+        div.my-3(data-hook="edit-domain-types-list")
+
+        button.btn.btn-outline-primary.box-shadow(data-hook="add-domain-type") Add Type
+
+      div.tab-pane(id="view-domain-types" data-hook="view-domain-types")
+
+        hr
+
+        div.mx-1.row.head.align-items-baseline
+
+          div.col-sm-3
+
+            h6.inline <b>Name</b>
+
+          div.col-sm-3
+
+            h6.inline <b>Numbe of Particles</b>
+
+          div.col-sm-6
+
+            h6.inline <b>Defaults</b>
+
+        div.my-3(data-hook="view-domain-types-list")
\ No newline at end of file
diff --git a/client/domain-view/templates/viewType.pug b/client/domain-view/templates/viewType.pug
new file mode 100644
index 0000000000..a5953f40cb
--- /dev/null
+++ b/client/domain-view/templates/viewType.pug
@@ -0,0 +1,38 @@
+div.mx-1
+
+  if(this.model.collection.indexOf(this.model) !== 1)
+    hr
+
+  div.row
+
+    div.col-sm-3
+
+      div=this.model.name
+
+    div.col-sm-3
+
+      div=this.model.numParticles
+
+    div.col-sm-6
+
+      div.row
+
+        div.col-sm-6
+
+          div="Mass: " + this.model.mass
+
+          div="Volume: " + this.model.volume
+
+          div="Density: " + this.model.rho
+
+        div.col-sm-6
+
+          div="Viscosity: " + this.model.nu
+
+          div="Speed of Sound: " + this.model.c
+
+          div
+
+            span.mr-3(for="view-td-fixed") Fixed:
+
+            input(type="checkbox" data-hook="view-td-fixed" disabled)
\ No newline at end of file
diff --git a/client/domain-view/views/edit-3D-domain-view.js b/client/domain-view/views/edit-3D-domain-view.js
new file mode 100644
index 0000000000..d1f1f585b1
--- /dev/null
+++ b/client/domain-view/views/edit-3D-domain-view.js
@@ -0,0 +1,302 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let path = require('path');
+//support files
+let app = require('../../app');
+let tests = require('../../views/tests');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+let SelectView = require('ampersand-select-view');
+//templates
+let template = require('../templates/edit3DDomainView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'change [data-target=edit-3d-domain-n]' : 'handleNumParticlesUpdate',
+    'change [data-target=edit-3d-domain-limitation]' : 'handleLimitsUpdate',
+    'change [data-hook=edit-3d-domain-type-select]' : 'handleTypeUpdate',
+    'change [data-target=edit-3d-domain-trans]' : 'handleTransformationupdate',
+    'click [data-hook=collapse-3D-domain-advanced]' : 'changeCollapseButtonText',
+    'click [data-hook=build-3d-domain]' : 'handleBuildDomain'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.data = {
+      "nx":1, "ny":1, "nz":1,
+      "xLim":[0, 0], "yLim":[0, 0], "zLim":[0, 0],
+      "type": null, "transformation": null
+    }
+    this.transformation = [0, 0, 0];
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    this.type = this.parent.model.types.get(0, "typeID");
+    this.updateTotalParticles();
+    this.updateTypeDefaults();
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e);
+  },
+  completeAction: function () {
+    $(this.queryByHook("c3dd-in-progress")).css("display", "none");
+    $(this.queryByHook("c3dd-complete")).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook("c3dd-complete")).css("display", "none");
+    }, 5000);
+  },
+  errorAction: function (action) {
+    $(this.queryByHook("c3dd-in-progress")).css("display", "none");
+    $(this.queryByHook("c3dd-action-error")).text(action);
+    $(this.queryByHook("c3dd-error")).css("display", "block");
+  },
+  handleBuildDomain: function () {
+    this.startAction();
+    this.transformation.every((value) => {
+      if(value !== 0) {
+        this.data.transformation = this.transformation;
+        return false;
+      }
+      return true;
+    });
+    this.data.domainExists = this.parent.model.particles.length > 0;
+    let endpoint = path.join(app.getApiPath(), "spatial-model/3d-domain");
+    app.postXHR(endpoint, this.data, {
+      success: (err, response, body) => {
+        this.parent.add3DDomain(body.limits, body.particles, body.figure);
+        this.completeAction();
+        $('html, body').animate({
+            scrollTop: $("#domain-figure").offset().top
+        }, 20);
+      },
+      error: (err, response, body) => {
+        this.errorAction(body.Message);
+      }
+    });
+  },
+  handleLimitsUpdate: function (e) {
+    let key = e.target.parentElement.parentElement.dataset.name;
+    let index = Number(e.target.parentElement.parentElement.dataset.index);
+    this.data[key][index] = Number(e.target.value);
+  },
+  handleNumParticlesUpdate: function (e) {
+    let key = e.target.parentElement.parentElement.dataset.key;
+    this.data[key] = Number(e.target.value);
+    this.updateTotalParticles();
+  },
+  handleTransformationupdate: function (e) {
+    let index = e.target.parentElement.parentElement.dataset.index;
+    this.transformation[index] = Number(e.target.value);
+  },
+  handleTypeUpdate: function (e) {
+    let typeID = Number(e.target.value);
+    this.type = this.parent.model.types.get(typeID, "typeID");
+    this.updateTypeDefaults();
+  },
+  startAction: function () {
+    $(this.queryByHook("c3dd-complete")).css("display", "none");
+    $(this.queryByHook("c3dd-error")).css("display", "none");
+    $(this.queryByHook("c3dd-in-progress")).css("display", "inline-block");
+  },
+  update: function () {},
+  updateValid: function () {},
+  updateTotalParticles: function () {
+    let n = this.data.nx * this.data.ny * this.data.nz;
+    $(this.queryByHook("3d-domain-n")).text(n);
+    $(this.queryByHook("build-3d-domain")).prop("disabled", n <= 0);
+  },
+  updateTypeDefaults: function () {
+    this.data.typeID = this.type.typeID;
+    this.data.type = {
+      "type_id": this.type.name, "mass": this.type.mass, "rho": this.type.rho, 
+      "nu": this.type.nu, "c": this.type.c, "fixed": this.type.fixed
+    }
+    $(this.queryByHook("edit-3d-domain-td-mass")).text(this.type.mass);
+    $(this.queryByHook("edit-3d-domain-td-vol")).text(this.type.volume);
+    $(this.queryByHook("edit-3d-domain-td-rho")).text(this.type.rho);
+    $(this.queryByHook("edit-3d-domain-td-nu")).text(this.type.nu);
+    $(this.queryByHook("edit-3d-domain-td-c")).text(this.type.c);
+    $(this.queryByHook("edit-3d-domain-td-fixed")).prop('checked', this.type.fixed);
+  },
+  subviews: {
+    nXInputView: {
+      hook: "edit-3d-domain-nx",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'nx',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.data.nx
+        });
+      }
+    },
+    nYInputView: {
+      hook: "edit-3d-domain-ny",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'ny',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.data.ny
+        });
+      }
+    },
+    nZInputView: {
+      hook: "edit-3d-domain-nz",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'nz',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.data.nz
+        });
+      }
+    },
+    xMinLimInputView: {
+      hook: "edit-3d-domain-x-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-lim-min',
+          valueType: 'number',
+          value: this.data.xLim[0]
+        });
+      }
+    },
+    yMinLimInputView: {
+      hook: "edit-3d-domain-y-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-lim-min',
+          valueType: 'number',
+          value: this.data.yLim[0]
+        });
+      }
+    },
+    zMinLimInputView: {
+      hook: "edit-3d-domain-z-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-lim-min',
+          valueType: 'number',
+          value: this.data.zLim[0]
+        });
+      }
+    },
+    xMaxLimInputView: {
+      hook: "edit-3d-domain-x-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-lim-max',
+          valueType: 'number',
+          value: this.data.xLim[1]
+        });
+      }
+    },
+    yMaxLimInputView: {
+      hook: "edit-3d-domain-y-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-lim-max',
+          valueType: 'number',
+          value: this.data.yLim[1]
+        });
+      }
+    },
+    zMaxLimInputView: {
+      hook: "edit-3d-domain-z-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-lim-max',
+          valueType: 'number',
+          value: this.data.zLim[1]
+        });
+      }
+    },
+    typeSelectView: {
+      hook: "edit-3d-domain-type-select",
+      prepareView: function (el) {
+        return new SelectView({
+          name: 'type',
+          required: true,
+          idAttribute: 'typeID',
+          textAttribute: 'name',
+          eagerValidate: true,
+          options: this.parent.model.types,
+          value: this.type
+        });
+      }
+    },
+    xTransInputView: {
+      hook: "edit-3d-domain-x-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-transformation',
+          valueType: 'number',
+          value: this.transformation[0]
+        });
+      }
+    },
+    yTransInputView: {
+      hook: "edit-3d-domain-y-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-transformation',
+          valueType: 'number',
+          value: this.transformation[1]
+        });
+      }
+    },
+    zTransInputView: {
+      hook: "edit-3d-domain-z-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-transformation',
+          valueType: 'number',
+          value: this.transformation[2]
+        });
+      }
+    }
+  }
+});
\ No newline at end of file
diff --git a/client/domain-view/views/import-mesh-view.js b/client/domain-view/views/import-mesh-view.js
new file mode 100644
index 0000000000..29bf950f57
--- /dev/null
+++ b/client/domain-view/views/import-mesh-view.js
@@ -0,0 +1,187 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let path = require('path');
+//support files
+let app = require('../../app');
+let tests = require('../../views/tests');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+let SelectView = require('ampersand-select-view');
+//templates
+let template = require('../templates/importMeshView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'change #meshfile' : 'setMeshFile',
+    'change #typefile' : 'setTypeFile',
+    'change [data-hook=import-mesh-type-select]' : 'handleTypeUpdate',
+    'change [data-target=import-mesh-trans]' : 'handleTransformationUpdate',
+    'click [data-hook=collapse-import-mesh-advanced]' : 'changeCollapseButtonText',
+    'click [data-hook=import-mesh-particles]' : 'handleImportMesh'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.meshFile = null;
+    this.typeFile = null;
+    this.data = {"type": null, "transformation": null};
+    this.transformation = [0, 0, 0];
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    this.type = this.parent.model.types.get(0, "typeID");
+    this.updateTypeDefaults();
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e);
+  },
+  completeAction: function () {
+    $(this.queryByHook("imp-in-progress")).css("display", "none");
+    $(this.queryByHook("imp-complete")).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook("imp-complete")).css("display", "none");
+    }, 5000);
+  },
+  errorAction: function (action) {
+    $(this.queryByHook("imp-in-progress")).css("display", "none");
+    $(this.queryByHook("imp-action-error")).text(action);
+    $(this.queryByHook("imp-error")).css("display", "block");
+  },
+  handleImportMesh: function () {
+    this.startAction();
+    this.transformation.every((value) => {
+      if(value !== 0) {
+        this.data.transformation = this.transformation;
+        return false;
+      }
+      return true;
+    });
+    let formData = new FormData();
+    formData.append("datafile", this.meshFile);
+    formData.append("particleData", JSON.stringify(this.data));
+    if(this.typeFile) {
+      formData.append("typefile", this.typeFile);
+    }
+    let endpoint = path.join(app.getApiPath(), 'spatial-model/import-mesh');
+    app.postXHR(endpoint, formData, {
+      success: (err, response, body) => {
+        body = JSON.parse(body);
+        this.parent.addMeshDomain(body.limits, body.particles, body.types, this.parent.model.particles.length > 0);
+        this.completeAction();
+        $('html, body').animate({
+            scrollTop: $("#domain-figure").offset().top
+        }, 20);
+      },
+      error: (err, response, body) => {
+        body = JSON.parse(body);
+        this.errorAction(body.Message);
+      }
+    }, false);
+  },
+  handleTransformationUpdate: function (e) {
+    let index = e.target.parentElement.parentElement.dataset.index;
+    this.transformation[index] = Number(e.target.value);
+  },
+  handleTypeUpdate: function (e) {
+    let typeID = Number(e.target.value);
+    this.type = this.parent.model.types.get(typeID, "typeID");
+    this.updateTypeDefaults();
+  },
+  setMeshFile: function (e) {
+    this.meshFile = e.target.files[0];
+    $(this.queryByHook("import-mesh-particles")).prop('disabled', !this.meshFile);
+  },
+  setTypeFile: function (e) {
+    this.typeFile = e.target.files[0];
+  },
+  startAction: function () {
+    $(this.queryByHook("imp-complete")).css("display", "none");
+    $(this.queryByHook("imp-error")).css("display", "none");
+    $(this.queryByHook("imp-in-progress")).css("display", "inline-block");
+  },
+  update: function () {},
+  updateValid: function () {},
+  updateTypeDefaults: function () {
+    this.data.typeID = this.type.typeID;
+    this.data.type = {
+      "type_id": this.type.name, "mass": this.type.mass, "rho": this.type.rho, 
+      "nu": this.type.nu, "c": this.type.c, "fixed": this.type.fixed
+    }
+    $(this.queryByHook("import-mesh-td-mass")).text(this.type.mass);
+    $(this.queryByHook("import-mesh-td-vol")).text(this.type.volume);
+    $(this.queryByHook("import-mesh-td-rho")).text(this.type.rho);
+    $(this.queryByHook("import-mesh-td-nu")).text(this.type.nu);
+    $(this.queryByHook("import-mesh-td-c")).text(this.type.c);
+    $(this.queryByHook("import-mesh-td-fixed")).prop('checked', this.type.fixed);
+  },
+  subviews: {
+    typeSelectView: {
+      hook: "import-mesh-type-select",
+      prepareView: function (el) {
+        return new SelectView({
+          name: 'type',
+          required: true,
+          idAttribute: 'typeID',
+          textAttribute: 'name',
+          eagerValidate: true,
+          options: this.parent.model.types,
+          value: this.type
+        });
+      }
+    },
+    xTransInputView: {
+      hook: "import-mesh-x-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-transformation',
+          valueType: 'number',
+          value: this.transformation[0]
+        });
+      }
+    },
+    yTransInputView: {
+      hook: "import-mesh-y-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-transformation',
+          valueType: 'number',
+          value: this.transformation[1]
+        });
+      }
+    },
+    zTransInputView: {
+      hook: "import-mesh-z-trans",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-transformation',
+          valueType: 'number',
+          value: this.transformation[2]
+        });
+      }
+    }
+  }
+});
\ No newline at end of file
diff --git a/client/domain-view/views/limits-view.js b/client/domain-view/views/limits-view.js
new file mode 100644
index 0000000000..09f740b160
--- /dev/null
+++ b/client/domain-view/views/limits-view.js
@@ -0,0 +1,162 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+//support files
+let app = require('../../app');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+//templates
+let template = require('../templates/limitsView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'click [data-hook=collapse-domain-limits]' : 'changeCollapseButtonText',
+    'change [data-target=limitation]' : 'setLimitation',
+    'change [data-target=reflect]' : 'setBoundaryCondition'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.readOnly = attrs.readOnly ? attrs.readOnly : false;
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    if(this.readOnly) {
+      $(this.queryByHook('domain-limits-edit-tab')).addClass("disabled");
+      $(".nav .disabled>a").on("click", function(e) {
+        e.preventDefault();
+        return false;
+      });
+      $(this.queryByHook('domain-limits-view-tab')).tab('show');
+      $(this.queryByHook('edit-domain-limits')).removeClass('active');
+      $(this.queryByHook('view-domain-limits')).addClass('active');
+    }else{
+      this.renderXMinLimitInputView();
+      this.renderYMinLimitInputView();
+      this.renderZMinLimitInputView();
+      this.renderXMaxLimitInputView();
+      this.renderYMaxLimitInputView();
+      this.renderZMaxLimitInputView();
+      $(this.queryByHook("reflect_x")).prop("checked", this.model.boundary_condition.reflect_x);
+      $(this.queryByHook("reflect_y")).prop("checked", this.model.boundary_condition.reflect_y);
+      $(this.queryByHook("reflect_z")).prop("checked", this.model.boundary_condition.reflect_z);
+    }
+    $(this.queryByHook("view-reflect_x")).prop("checked", this.model.boundary_condition.reflect_x);
+    $(this.queryByHook("view-reflect_y")).prop("checked", this.model.boundary_condition.reflect_y);
+    $(this.queryByHook("view-reflect_z")).prop("checked", this.model.boundary_condition.reflect_z);
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e);
+  },
+  renderXMinLimitInputView: function () {
+    if(this.xMinLimitInputView) {
+      this.xMinLimitInputView.remove();
+    }
+    this.xMinLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'x-lim-min',
+      valueType: 'number',
+      value: this.model.x_lim[0] || 0
+    });
+    app.registerRenderSubview(this, this.xMinLimitInputView, "x-lim-min");
+  },
+  renderYMinLimitInputView: function () {
+    if(this.yMinLimitInputView) {
+      this.yMinLimitInputView.remove();
+    }
+    this.yMinLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'y-lim-min',
+      valueType: 'number',
+      value: this.model.y_lim[0] || 0
+    });
+    app.registerRenderSubview(this, this.yMinLimitInputView, "y-lim-min");
+  },
+  renderZMinLimitInputView: function () {
+    if(this.zMinLimitInputView) {
+      this.zMinLimitInputView.remove();
+    }
+    this.zMinLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'z-lim-min',
+      valueType: 'number',
+      value: this.model.z_lim[0] || 0
+    });
+    app.registerRenderSubview(this, this.zMinLimitInputView, "z-lim-min");
+  },
+  renderXMaxLimitInputView: function () {
+    if(this.xMaxLimitInputView) {
+      this.xMaxLimitInputView.remove();
+    }
+    this.xMaxLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'x-lim-max',
+      valueType: 'number',
+      value: this.model.x_lim[1] || 0
+    });
+    app.registerRenderSubview(this, this.xMaxLimitInputView, "x-lim-max");
+  },
+  renderYMaxLimitInputView: function () {
+    if(this.yMaxLimitInputView) {
+      this.yMaxLimitInputView.remove();
+    }
+    this.yMaxLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'y-lim-max',
+      valueType: 'number',
+      value: this.model.y_lim[1] || 0
+    });
+    app.registerRenderSubview(this, this.yMaxLimitInputView, "y-lim-max");
+  },
+  renderZMaxLimitInputView: function () {
+    if(this.zMaxLimitInputView) {
+      this.zMaxLimitInputView.remove();
+    }
+    this.zMaxLimitInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'z-lim-max',
+      valueType: 'number',
+      value: this.model.z_lim[1] || 0
+    });
+    app.registerRenderSubview(this, this.zMaxLimitInputView, "z-lim-max");
+  },
+  setBoundaryCondition: function (e) {
+    let key = e.target.dataset.hook;
+    this.model.boundary_condition[key] = e.target.checked;
+    this.updateView();
+  },
+  setLimitation: function (e) {
+    let key = e.target.parentElement.parentElement.dataset.name;
+    let index = Number(e.target.parentElement.parentElement.dataset.index);
+    this.model[key][index] = Number(e.target.value.trim());
+    this.updateView();
+  },
+  update: function () {},
+  updateValid: function () {},
+  updateView: function () {
+    this.parent.renderLimitsView();
+  }
+});
diff --git a/client/domain-view/views/particle-view.js b/client/domain-view/views/particle-view.js
new file mode 100644
index 0000000000..87f1a0b424
--- /dev/null
+++ b/client/domain-view/views/particle-view.js
@@ -0,0 +1,229 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+//support files
+let app = require('../../app');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+let SelectView = require('ampersand-select-view');
+//templates
+let template = require('../templates/editParticleView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: function () {
+    let events = {};
+    events[`change [data-hook=particle-type-${this.viewIndex}]`] = 'handleSelectType';
+    events[`change [data-target=location-${this.viewIndex}]`] = 'handleUpdateLocation';
+    events[`change [data-hook=particle-fixed=${this.viewIndex}]`] = 'handleUpdateFixed';
+    return events;
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.viewIndex = attrs.viewIndex;
+    this.defaultType = attrs.defaultType;
+    this.disable = attrs.disable ? attrs.disable : false;
+    this.origType = this.model.type;
+    this.origPoint = JSON.parse(JSON.stringify(this.model.point));
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    this.renderTypeSelectView();
+    this.renderParticleProperties();
+    this.renderXCoordView();
+    this.renderYCoordView();
+    this.renderZCoordView();
+  },
+  handleSelectType: function (e) {
+    this.defaultType = this.parent.model.types.get(this.model.type, "typeID")
+    this.model.type = Number(e.target.value);
+    let type = this.parent.model.types.get(this.model.type, "typeID")
+    if(this.model.mass === this.defaultType.mass) {
+      this.model.mass = type.mass;
+    }
+    if(this.model.volume === this.defaultType.volume) {
+      this.model.volume = type.volume;
+    }
+    if(this.model.rho === this.defaultType.rho) {
+      this.model.rho = type.rho;
+    }
+    if(this.model.nu === this.defaultType.nu) {
+      this.model.nu = type.nu;
+    }
+    if(this.model.c === this.defaultType.c) {
+      this.model.c = type.c;
+    }
+    if(this.model.fixed === this.defaultType.fixed) {
+      this.model.fixed = type.fixed;
+    }
+    this.renderParticleProperties();
+  },
+  handleUpdateFixed: function (e) {
+    this.model.fixed = e.target.checked;
+  },
+  handleUpdateLocation: function (e) {
+    let index = Number(e.target.parentElement.parentElement.dataset.index);
+    this.model.point[index] = Number(e.target.value);
+  },
+  renderCInputView: function () {
+    if(this.cInputView) {
+      this.cInputView.remove();
+    }
+    this.cInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'speed-of-sound',
+      disabled: this.disable,
+      modelKey: 'c',
+      valueType: 'number',
+      value: this.model.c
+    });
+    app.registerRenderSubview(this, this.cInputView, `particle-c-${this.viewIndex}`);
+  },
+  renderParticleProperties: function () {
+    this.renderCInputView();
+    this.renderMassInputView();
+    this.renderNuInputView();
+    this.renderRhoInputView();
+    this.renderVolumeInputView();
+    $(this.queryByHook(`particle-fixed-${this.viewIndex}`)).prop('checked', this.model.fixed);
+    $(this.queryByHook(`particle-fixed-${this.viewIndex}`)).prop('disabled', this.disable);
+  },
+  renderMassInputView: function () {
+    if(this.massInputView) {
+      this.massInputView.remove();
+    }
+    this.massInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'mass',
+      disabled: this.disable,
+      modelKey: 'mass',
+      valueType: 'number',
+      value: this.model.mass
+    });
+    app.registerRenderSubview(this, this.massInputView, `particle-mass-${this.viewIndex}`);
+  },
+  renderNuInputView: function () {
+    if(this.nuInputView) {
+      this.nuInputView.remove();
+    }
+    this.nuInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'viscosity',
+      disabled: this.disable,
+      modelKey: 'nu',
+      valueType: 'number',
+      value: this.model.nu
+    });
+    app.registerRenderSubview(this, this.nuInputView, `particle-nu-${this.viewIndex}`);
+  },
+  renderRhoInputView: function () {
+    if(this.rhoInputView) {
+      this.rhoInputView.remove();
+    }
+    this.rhoInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'density',
+      disabled: this.disable,
+      modelKey: 'rho',
+      valueType: 'number',
+      value: this.model.rho
+    });
+    app.registerRenderSubview(this, this.rhoInputView, `particle-rho-${this.viewIndex}`);
+  },
+  renderTypeSelectView: function () {
+    if(this.typeSelectView) {
+      this.typeSelectView.remove();
+    }
+    this.typeSelectView = new SelectView({
+      name: 'type',
+      required: true,
+      idAttribute: 'typeID',
+      textAttribute: 'name',
+      eagerValidate: true,
+      options: this.parent.model.types,
+      value: this.parent.model.types.get(this.model.type, "typeID")
+    });
+    app.registerRenderSubview(this, this.typeSelectView, `particle-type-${this.viewIndex}`)
+    $(this.queryByHook(`particle-type-${this.viewIndex}`)).find('select').prop('disabled', this.disable);
+  },
+  renderVolumeInputView: function () {
+    if(this.volumeInputView) {
+      this.volumeInputView.remove();
+    }
+    this.volumeInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'volume',
+      disabled: this.disable,
+      modelKey: 'volume',
+      valueType: 'number',
+      value: this.model.volume
+    });
+    app.registerRenderSubview(this, this.volumeInputView, `particle-vol-${this.viewIndex}`);
+  },
+  renderXCoordView: function () {
+    if(this.xCoordView) {
+      this.xCoordView.remove();
+    }
+    this.xCoordView = new InputView({
+      parent: this,
+      required: true,
+      name: 'x-coord',
+      disabled: this.disable,
+      valueType: 'number',
+      value: this.model.point[0]
+    });
+    app.registerRenderSubview(this, this.xCoordView, `x-coord-${this.viewIndex}`);
+  },
+  renderYCoordView: function () {
+    if(this.yCoordView) {
+      this.yCoordView.remove();
+    }
+    this.yCoordView = new InputView({
+      parent: this,
+      required: true,
+      name: 'y-coord',
+      disabled: this.disable,
+      valueType: 'number',
+      value: this.model.point[1]
+    });
+    app.registerRenderSubview(this, this.yCoordView, `y-coord-${this.viewIndex}`);
+  },
+  renderZCoordView: function () {
+    if(this.zCoordView) {
+      this.zCoordView.remove();
+    }
+    this.zCoordView = new InputView({
+      parent: this,
+      required: true,
+      name: 'z-coord',
+      disabled: this.disable,
+      valueType: 'number',
+      value: this.model.point[2]
+    });
+    app.registerRenderSubview(this, this.zCoordView, `z-coord-${this.viewIndex}`);
+  },
+  update: function (e) {},
+  updateValid: function (e) {}
+});
\ No newline at end of file
diff --git a/client/domain-view/views/properties-view.js b/client/domain-view/views/properties-view.js
new file mode 100644
index 0000000000..f45575c57c
--- /dev/null
+++ b/client/domain-view/views/properties-view.js
@@ -0,0 +1,176 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+//support files
+let app = require('../../app');
+let Tooltips = require('../../tooltips');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+//templates
+let template = require('../templates/propertiesView.pug');
+
+module.exports = View.extend({
+  events: {
+    'click [data-hook=collapse-domain-properties]' : 'changeCollapseButtonText',
+    'change [data-hook=static-domain]' : 'setStaticDomain',
+    'change [data-hook=density]' : 'setDensity',
+    'change [data-target=gravity]' : 'setGravity',
+    'change [data-hook=pressure]' : 'setPressure',
+    'change [data-hook=speed]' : 'setSpeed'
+  },
+  template: template,
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.readOnly = attrs.readOnly ? attrs.readOnly : false;
+    this.tooltips = Tooltips.domainEditor;
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    if(this.readOnly) {
+      $(this.queryByHook('domain-properties-edit-tab')).addClass("disabled");
+      $(".nav .disabled>a").on("click", function(e) {
+        e.preventDefault();
+        return false;
+      });
+      $(this.queryByHook('domain-properties-view-tab')).tab('show');
+      $(this.queryByHook('edit-domain-properties')).removeClass('active');
+      $(this.queryByHook('view-domain-properties')).addClass('active');
+    }else{
+      $(this.queryByHook("static-domain")).prop("checked", this.model.static);
+      this.renderDensityInputView();
+      this.renderXGravityInputView();
+      this.renderYGravityInputView();
+      this.renderZGravityInputView();
+      this.renderPressureInputView();
+      this.renderSpeedInputView();
+    }
+    $(this.queryByHook("view-static-domain")).prop("checked", this.model.static);
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e);
+  },
+  renderDensityInputView: function () {
+    if(this.densityInputView) {
+      this.densityInputView.remove();
+    }
+    this.densityInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'density',
+      valueType: 'number',
+      value: this.model.rho_0 || 1
+    });
+    app.registerRenderSubview(this, this.densityInputView, "density");
+  },
+  renderPressureInputView: function () {
+    if(this.pressureInputView) {
+      this.pressureInputView.remove();
+    }
+    this.pressureInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'pressure',
+      valueType: 'number',
+      value: this.model.p_0 || 0
+    });
+    app.registerRenderSubview(this, this.pressureInputView, "pressure");
+  },
+  renderSpeedInputView: function () {
+    if(this.speedInputView) {
+      this.speedInputView.remove();
+    }
+    this.speedInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'speed',
+      valueType: 'number', 
+      value: this.model.c_0 || 0
+    });
+    app.registerRenderSubview(this, this.speedInputView, "speed");
+  },
+  renderXGravityInputView: function () {
+    if(this.xGravityInputView) {
+      this.xGravityInputView.remove();
+    }
+    this.xGravityInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'gravity-x',
+      valueType: 'number',
+      value: this.model.gravity[0],
+      label: "X:  "
+    });
+    app.registerRenderSubview(this, this.xGravityInputView, "gravity-x");
+  },
+  renderYGravityInputView: function () {
+    if(this.yGravityInputView) {
+      this.yGravityInputView.remove();
+    }
+    this.yGravityInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'gravity-y',
+      valueType: 'number',
+      value: this.model.gravity[1],
+      label: "Y:  "
+    });
+    app.registerRenderSubview(this, this.yGravityInputView, "gravity-y");
+  },
+  renderZGravityInputView: function () {
+    if(this.zGravityInputView) {
+      this.zGravityInputView.remove();
+    }
+    this.zGravityInputView = new InputView({
+      parent: this,
+      required: true,
+      name: 'gravity-z',
+      valueType: 'number',
+      value: this.model.gravity[2],
+      label: "Z:  "
+    });
+    app.registerRenderSubview(this, this.zGravityInputView, "gravity-z");
+  },
+  setDensity: function (e) {
+    this.model.rho_0 = Number(e.target.value);
+    this.updateView();
+  },
+  setGravity: function (e) {
+    let index = Number(e.target.parentElement.parentElement.dataset.index);
+    this.model.gravity[index] = Number(e.target.value);
+    this.updateView();
+  },
+  setPressure: function (e) {
+    this.model.p_0 = Number(e.target.value);
+    this.updateView();
+  },
+  setSpeed: function (e) {
+    this.model.c_0 = Number(e.target.value);
+    this.updateView();
+  },
+  setStaticDomain: function (e) {
+    this.model.static = e.target.checked;
+    this.updateView();
+  },
+  update: function (e) {},
+  updateValid: function (e) {},
+  updateView: function (e) {
+    this.parent.renderPropertiesView();
+  }
+});
\ No newline at end of file
diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
new file mode 100644
index 0000000000..c5376bb788
--- /dev/null
+++ b/client/domain-view/views/type-view.js
@@ -0,0 +1,178 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let _ = require('underscore');
+//support files
+let app = require('../../app');
+let tests = require('../../views/tests');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+//templates
+let editTemplate = require('../templates/editType.pug');
+let viewTemplate = require('../templates/viewType.pug');
+
+module.exports = View.extend({
+  bindings: {
+    'model.selected' : {
+      type: function (el, value, previousValue) {
+        el.checked = value;
+      },
+      hook: 'select'
+    }
+  },
+  events: {
+    'change [data-hook=type-name]' : 'handleRenameType',
+    'change [data-target=type-defaults]' : 'updateView',
+    'click [data-hook=select]' : 'selectType',
+    'click [data-hook=unassign-all]' : 'handleUnassignParticles',
+    'click [data-hook=delete-type]' : 'handleDeleteType',
+    'click [data-hook=delete-all]' : 'handleDeleteTypeAndParticle',
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.vieWMode = attrs.viewMode ? attrs.viewMode : false;
+  },
+  render: function (attrs, options) {
+    this.template = this.vieWMode ? viewTemplate : editTemplate;
+    View.prototype.render.apply(this, arguments);
+    if(!this.vieWMode) {
+      if(this.model.selected) {
+        setTimeout(_.bind(this.openTypeDetails, this), 1);
+      }
+    }
+    app.documentSetup();
+  },
+  handleDeleteType: function (e) {
+    let type = Number(e.target.dataset.type);
+    this.model.collection.removeType(this.model);
+    this.parent.parent.deleteType(this.model.typeID);
+  },
+  handleDeleteTypeAndParticle: function (e) {
+    let type = Number(e.target.dataset.type);
+    this.model.collection.removeType(this.model);
+    this.parent.parent.deleteType(this.model.typeID, {unassign: false});
+  },
+  handleRenameType: function (e) {
+    this.updateView();
+    let type = Number(e.target.parentElement.parentElement.dataset.target);
+    let name = e.target.value;
+    this.parent.parent.renameType(type, name);
+  },
+  handleUnassignParticles: function () {
+    this.model.numParticles = 0;
+    this.parent.parent.unassignAllParticles(this.model.typeID);
+  },
+  openTypeDetails: function () {
+    $("#collapse-type-details" + this.model.typeID).collapse("show");
+  },
+  selectType: function () {
+    this.model.selected = !this.model.selected;
+  },
+  update: function () {},
+  updateValid: function () {},
+  updateView: function () {
+    this.parent.renderViewTypeView();
+  },
+  subviews: {
+    inputTypeID: {
+      hook: "type-name",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'name',
+          modelKey: 'name',
+          valueType: 'string',
+          value: this.model.name
+        });
+      }
+    },
+    inputMass: {
+      hook: "td-mass",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'mass',
+          modelKey: 'mass',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.model.mass
+        });
+      }
+    },
+    inputVolume: {
+      hook: 'td-vol',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'volume',
+          modelKey: 'volume',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.model.volume
+        });
+      }
+    },
+    inputDensity: {
+      hook: 'td-rho',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'density',
+          modelKey: 'rho',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.model.rho
+        });
+      }
+    },
+    inputViscosity: {
+      hook: 'td-nu',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'viscosity',
+          modelKey: 'nu',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.model.nu
+        });
+      }
+    },
+    inputSpeedOfSound: {
+      hook: 'td-c',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'speed-of-sound',
+          modelKey: 'c',
+          valueType: 'number',
+          tests: tests.valueTests,
+          value: this.model.c
+        });
+      }
+    }
+  }
+});
\ No newline at end of file
diff --git a/client/domain-view/views/types-description-view.js b/client/domain-view/views/types-description-view.js
new file mode 100644
index 0000000000..2279ff68ee
--- /dev/null
+++ b/client/domain-view/views/types-description-view.js
@@ -0,0 +1,128 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let path = require('path');
+//support files
+let app = require('../../app');
+//views
+let View = require('ampersand-view');
+let SelectView = require('ampersand-select-view');
+//templates
+let template = require('../templates/typesDescriptionView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'change [data-hook=file-select]' : 'selectTypeFile',
+    'change [data-hook=file-location-select]' : 'selectFileLocation',
+    'click [data-hook=set-particle-types-btn]' : 'getTypesFromFile'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.typeFile = null;
+  },
+  render: function(attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    let endpoint = path.join(app.getApiPath(), 'spatial-model/types-list');
+    app.getXHR(endpoint, {success: (err, response, body) => {
+      this.typeFiles = body.files;
+      this.fileLocations = body.paths;
+      this.renderFileSelectView();
+    }});
+  },
+  completeAction: function () {
+    $(this.queryByHook('st-in-progress')).css('display', 'none');
+    $(this.queryByHook('st-complete')).css('display', 'inline-block');
+  },
+  errorAction: function (action) {
+    $(this.queryByHook('st-in-progress')).css('display', 'none');
+    $(this.queryByHook('st-action-error')).text(action);
+    $(this.queryByHook('st-error')).css('display', 'block');
+  },
+  getTypesFromFile: function () {
+    this.startAction();
+    let queryStr = `?path=${this.typeFile}`;
+    let endpoint = path.join(app.getApiPath(), 'spatial-model/particle-types') + queryStr;
+    app.getXHR(endpoint, {
+      success: (err, response, body) => {
+        this.parent.setParticleTypes(body.names, body.types);
+        this.completeAction();
+      },
+      error: (err, response, body) => {
+        this.errorAction(body.Message);
+      }
+    });
+  },
+  renderFileLocationSelectView: function (options) {
+    if(this.fileLocationSelectView) {
+      this.fileLocationSelectView.remove();
+    }
+    this.fileLocationSelectView = new SelectView({
+      name: 'type-locations',
+      required: false,
+      idAttributes: 'cid',
+      options: options,
+      unselectedText: "-- Select Location --"
+    });
+    app.registerRenderSubview(this, this.fileLocationSelectView, "file-location-select");
+  },
+  renderFileSelectView: function () {
+    if(this.fileSelectView) {
+      this.fileSelectView.remove();
+    }
+    this.fileSelectView = new SelectView({
+      name: 'type-files',
+      required: false,
+      idAttributes: 'cid',
+      options: this.typeFiles,
+      unselectedText: "-- Select Type File --",
+    });
+    app.registerRenderSubview(this, this.fileSelectView, "file-select");
+  },
+  selectFileLocation: function (e) {
+    let value = e.target.value;
+    this.typeFile = value ? value : null;
+    $(this.queryByHook("set-particle-types-btn")).prop("disabled", this.typeFile === null);
+  },
+  selectTypeFile: function (e) {
+    let value = e.target.value;
+    if(value) {
+      if(this.fileLocations[value].length > 1) {
+        $(this.queryByHook("type-location-message")).css('display', "block");
+        $(this.queryByHook("file-location-container")).css("display", "inline-block");
+        this.renderFileLocationSelectView(this.fileLocations[value]);
+        this.typeFile = null;
+      }else{
+        $(this.queryByHook("type-location-message")).css('display', "none");
+        $(this.queryByHook("file-location-container")).css("display", "none");
+        this.typeFile = this.fileLocations[value][0];
+      }
+    }else{
+      $(this.queryByHook("type-location-message")).css('display', "none");
+      $(this.queryByHook("file-location-container")).css("display", "none");
+      this.typeFile = null;
+    }
+    $(this.queryByHook("set-particle-types-btn")).prop("disabled", this.typeFile === null);
+  },
+  startAction: function () {
+    $(this.queryByHook("st-complete")).css('display', 'none');
+    $(this.queryByHook("st-error")).css('display', 'none');
+    $(this.queryByHook("st-in-progress")).css("display", "inline-block");
+  },
+});
\ No newline at end of file
diff --git a/client/domain-view/views/types-view.js b/client/domain-view/views/types-view.js
new file mode 100644
index 0000000000..b5351ed9e9
--- /dev/null
+++ b/client/domain-view/views/types-view.js
@@ -0,0 +1,105 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+//support files
+let app = require('../../app');
+//views
+let View = require('ampersand-view');
+let TypeView = require('./type-view');
+//templates
+let template = require('../templates/typesView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'click [data-hook=collapse-domain-types]' : 'changeCollapseButtonText',
+    'click [data-hook=add-domain-type]' : 'handleAddDomainType',
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.readOnly = attrs.readOnly ? attrs.readOnly : false;
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    if(this.readOnly) {
+      $(this.queryByHook('domain-types-edit-tab')).addClass("disabled");
+      $(".nav .disabled>a").on("click", function(e) {
+        e.preventDefault();
+        return false;
+      });
+      $(this.queryByHook('domain-types-view-tab')).tab('show');
+      $(this.queryByHook('edit-domain-types')).removeClass('active');
+      $(this.queryByHook('view-domain-types')).addClass('active');
+    }else{
+      this.renderEditTypeView();
+    }
+    this.toggleDomainError();
+    this.renderViewTypeView();
+  },
+  changeCollapseButtonText: function (e) {
+    app.changeCollapseButtonText(this, e);
+  },
+  handleAddDomainType: function () {
+    let name = this.collection.addType();
+    this.parent.addType(name);
+  },
+  renderEditTypeView: function () {
+    if(this.editTypeView) {
+      this.editTypeView.remove();
+    }
+    let options = {
+      filter: function (model) {
+          return model.typeID != 0;
+      }
+    }
+    this.editTypeView = this.renderCollection(
+      this.collection,
+      TypeView,
+      this.queryByHook("edit-domain-types-list"),
+      options
+    );
+  },
+  renderViewTypeView: function () {
+    if(this.viewTypeView) {
+      this.viewTypeView.remove();
+    }
+    let options = {
+      viewOptions: {viewMode: true},
+      filter: function (model) {
+          return model.typeID != 0;
+      }
+    }
+    this.viewTypeView = this.renderCollection(
+      this.collection,
+      TypeView,
+      this.queryByHook("view-domain-types-list"),
+      options
+    );
+  },
+  toggleDomainError: function () {
+    let errorMsg = $(this.queryByHook('domain-error'))
+    if(!this.collection.parent.valid) {
+      errorMsg.addClass('component-invalid');
+      errorMsg.removeClass('component-valid');
+    }else{
+      errorMsg.addClass('component-valid');
+      errorMsg.removeClass('component-invalid');
+    }
+  }
+});
\ No newline at end of file

From fb173ee0952618685cb8a382aaeb3201b0c4ed39 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:28:27 -0400
Subject: [PATCH 036/110] Added a new template for domain plots.

---
 stochss_templates/domainPlotTemplate.json | 34 +++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 stochss_templates/domainPlotTemplate.json

diff --git a/stochss_templates/domainPlotTemplate.json b/stochss_templates/domainPlotTemplate.json
new file mode 100644
index 0000000000..4aea686316
--- /dev/null
+++ b/stochss_templates/domainPlotTemplate.json
@@ -0,0 +1,34 @@
+{
+	"data": [
+		{
+			"ids": [],
+			"marker": {
+				"color": "",
+				"size": 5
+			},
+			"mode": "markers",
+			"name": "",
+			"x": [],
+			"y": [],
+			"z": [],
+			"type": "scatter3d"
+		}
+	],
+	"layout": {
+		"width": null,
+		"height": null,
+		"scene": {
+			"aspectmode": "data"
+		},
+		"xaxis": {
+			"range": []
+		},
+		"yaxis": {
+			"range": []
+		},
+		"autosize": true
+	},
+	"config": {
+		"responsive": true
+	}
+}
\ No newline at end of file

From f042de41755b04a4f83e9511b2146cad1993a303 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:30:58 -0400
Subject: [PATCH 037/110] Added defaults for the new 'c' and 'rho' particle
 properties to default type.

---
 stochss_templates/nonSpatialModelTemplate.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stochss_templates/nonSpatialModelTemplate.json b/stochss_templates/nonSpatialModelTemplate.json
index ec682bfcf7..415672303f 100644
--- a/stochss_templates/nonSpatialModelTemplate.json
+++ b/stochss_templates/nonSpatialModelTemplate.json
@@ -25,10 +25,12 @@
         	"reflect_z": true},
         "types": [
             {
+                "c":10,
                 "fixed":false,
                 "mass":1.0,
                 "name":"Un-Assigned",
                 "nu":0.0,
+                "rho":1.0,
                 "typeID":0,
                 "volume":1.0
             }

From 252328e550e8b66c4f0418615870e36c5cdb0c63 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:47:39 -0400
Subject: [PATCH 038/110] Added tests to filter tests for particle type
 description files. Refactored the get domain plot functions to use the new
 domain plot template if the domain has no particles. Refactored the get
 particles from 3D domain functions to add a plot to the response if the
 domain had no particles. Added backward compatability checks for 'c' and
 'rho' to domain types. Fixed color selection for new plot traces. Fixed
 type_id assignment when building a stochss domain from a spatialpy domain.

---
 stochss/handlers/models.py                    | 10 ++-
 .../handlers/util/stochss_spatial_model.py    | 85 +++++++++++++------
 2 files changed, 65 insertions(+), 30 deletions(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 2dd2ab7d9a..4072f163af 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -174,9 +174,11 @@ async def get(self):
         log.info("Generating the domain plot")
         try:
             model = StochSSSpatialModel(path=path)
-            fig = json.loads(model.get_domain_plot(path=d_path, new=new))
+            fig, trace_temp = model.get_domain_plot(path=d_path, new=new)
             log.info("Loading the domain plot")
-            resp = {"fig":fig}
+            if isinstance(fig, str):
+                fig = json.loads(fig)
+            resp = {"fig":fig, "trace_temp": trace_temp}
             log.debug(f"Response: {resp}")
             self.write(resp)
         except StochSSAPIError as err:
@@ -346,7 +348,9 @@ async def get(self):
         self.set_header('Content-Type', 'application/json')
         try:
             folder = StochSSFolder(path="")
-            test = lambda ext, root, file: bool("trash" in root.split("/"))
+            test = lambda ext, root, file: bool(
+                "trash" in root.split("/") or file.startswith('.') or 'wkfl' in root
+            )
             resp = folder.get_file_list(ext=".txt", test=test)
             log.debug("Response: {resp}")
             self.write(resp)
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index be9b708eac..914424dc65 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -18,6 +18,7 @@
 
 import os
 import json
+import copy
 import string
 import hashlib
 import tempfile
@@ -126,7 +127,7 @@ def __build_stochss_domain_particles(cls, s_domain, data=None):
             else:
                 viscosity = data['type']['nu']
                 fixed = data['type']['fixed']
-                type_id = data['type']['typeID']
+                type_id = data['typeID']
             point = list(vertex)
             if data is not None and data['transformation'] is not None:
                 point = [coord + data['transformation'][i] for i, coord in enumerate(point)]
@@ -332,7 +333,7 @@ def __get_trace_data(cls, particles, name="", index=None):
             z_data.append(particle['point'][2])
         marker = {"size":5}
         if index is not None:
-            marker["color"] = common_rgb_values[(index - 1) % len(common_rgb_values)]
+            marker["color"] = common_rgb_values[(index) % len(common_rgb_values)]
         return plotly.graph_objs.Scatter3d(ids=ids, x=x_data, y=y_data, z=z_data,
                                            name=name, mode="markers", marker=marker)
 
@@ -373,12 +374,21 @@ def __update_domain(self):
             self.model['domain'] = self.get_model_template()['domain']
         elif "static" not in self.model['domain'].keys():
             self.model['domain']['static'] = True
+        if "rho" not in self.model['domain']['types'][0].keys() or \
+                    "c" not in self.model['domain']['types'][0].keys():
+            for d_type in self.model['domain']['types']:
+                if "rho" not in d_type.keys():
+                    d_type['rho'] = d_type['mass'] / d_type['volume']
+                if "c" not in d_type.keys():
+                    d_type['c'] = 10
         if self.model['domain']['particles']:
             if "rho" not in self.model['domain']['particles'][0].keys() or \
                         "c" not in self.model['domain']['particles'][0].keys():
                 for particle in self.model['domain']['particles']:
-                    particle['rho'] = particle['mass']/particle['volume']
-                    particle['c'] = 10
+                    if "rho" not in particle.keys():
+                        particle['rho'] = particle['mass'] / particle['volume']
+                    if "c" not in particle.keys():
+                        particle['c'] = 10
 
 
     def convert_to_model(self):
@@ -478,43 +488,64 @@ def get_domain_plot(self, path=None, new=False, domains=None):
         if domains is None:
             if new:
                 path = '/stochss/stochss_templates/nonSpatialModelTemplate.json'
+                s_domain = StochSSSpatialModel(path).load()['domain']
             elif path is None:
                 path = self.path
+                s_domain = self.load()['domain']
             try:
                 domain = Domain.read_stochss_domain(path)
             except DomainError as err:
                 raise DomainFormatError(f"Failed to load the domain.  Reason given: {err}") from err
         else:
             domain = domains[0]
+            s_domain = domains[1]
+        fig_temp_path = "/stochss/stochss_templates/domainPlotTemplate.json"
+        with open(fig_temp_path, "r") as fig_temp_file:
+            fig_temp = json.load(fig_temp_file)
+            trace_temp = copy.deepcopy(fig_temp['data'][0])
+        if len(s_domain['particles']) == 0:
+            fig_temp['data'][0]['name'] = "Un-Assigned"
+            # Case #1: no particles and one type
+            if len(s_domain['types']) == 1:
+                return fig_temp, trace_temp
+            # Case #2: no particles and multiple types
+            for index in range(1, len(s_domain['types'])):
+                trace = copy.deepcopy(trace_temp)
+                trace['name'] = s_domain['types'][index]['name']
+                fig_temp['data'].append(trace)
+            return fig_temp, trace_temp
         fig = domain.plot_types(return_plotly_figure=True)
-        if not fig['data']:
-            fig['data'].append(self.__get_trace_data(particles=[], name="Un-Assigned"), index=0)
+        # Case #3: 1 or more particles and one type
+        if len(s_domain['types']) == 1:
+            fig['data'][0]['name'] = "Un-Assigned"
+            ids = list(filter(lambda particle: particle['particle_id'], s_domain['particles']))
+            fig['data'][0]['ids'] = ids
+        # Case #4: 1 or more particles and multiple types
         else:
-            s_domain = self.load()['domain'] if domains is None else domains[1]
-            for i, d_type in enumerate(s_domain['types']):
-                if len(s_domain['types']) > 1:
-                    particles = list(filter(lambda particle, key=i: particle['type'] == key,
-                                            s_domain['particles']))
+            for index, d_type in enumerate(s_domain['types']):
+                if d_type['name'] == "Un-Assigned":
+                    t_test = lambda trace: trace['name'] in ("Un-Assigned", "UnAssigned")
                 else:
-                    particles = s_domain['particles']
-                ids = list(map(lambda particle: particle['particle_id'], particles))
-                index = list(filter(
-                    lambda trace, name=d_type['name']: trace['name'].endswith(name), fig['data']
-                ))
-                if len(index) !=0:
-                    index = fig['data'].index(index[0])
-                    fig['data'][index]['name'] = d_type['name']
-                    fig['data'][index]['ids'] = ids
+                    t_test = lambda trace, name=d_type['name']: trace['name'] == name
+                traces = list(filter(t_test, fig['data']))
+                if len(traces) == 0:
+                    fig['data'].insert(index, self.__get_trace_data(
+                        particles=[], name=d_type['name'], index=index
+                    ))
                 else:
-                    fig['data'].insert(
-                        i, self.__get_trace_data(particles=[], name=d_type['name'], index=i)
-                    )
-                    fig['data'][i]['ids'] = ids
+                    particles = list(filter(
+                        lambda particle, key=d_type['typeID']: particle['type'] == key,
+                        s_domain['particles']
+                    ))
+                    ids = list(map(lambda particle: particle['particle_id'], particles))
+                    trace = traces[0]
+                    trace['name'] = d_type['name']
+                    trace['ids'] = ids
         fig['layout']['width'] = None
         fig['layout']['height'] = None
         fig['layout']['autosize'] = True
         fig['config'] = {"responsive":True}
-        return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder)
+        return json.dumps(fig, cls=plotly.utils.PlotlyJSONEncoder), trace_temp
 
 
     def get_notebook_data(self):
@@ -559,12 +590,12 @@ def get_particles_from_3d_domain(self, data):
         else:
             s_domain = Domain.create_2D_domain(xlim=xlim, ylim=ylim,
                                                nx=data['nx'], ny=data['ny'], **data['type'])
-        domain = self.__build_stochss_domain(s_domain=s_domain)
+        domain = self.__build_stochss_domain(s_domain=s_domain, data=data)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
         resp = {"particles":domain['particles'], "limits":limits}
         if data['domainExists']:
             return resp
-        resp['figure'] = json.loads(self.get_domain_plot(domains=(s_domain, domain)))
+        resp['figure'] = json.loads(self.get_domain_plot(domains=(s_domain, domain))[0])
         return resp
 
 

From dd891f5e3b0a4712dff8e56f8cc2fd8c97963722 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:49:51 -0400
Subject: [PATCH 039/110] Added property to input view to allow it to be
 disabled on render.

---
 client/views/input.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/client/views/input.js b/client/views/input.js
index e4531e0732..3e2ba786cc 100644
--- a/client/views/input.js
+++ b/client/views/input.js
@@ -24,6 +24,7 @@ module.exports = AmpersandInputView.extend({
     label: 'string',
     modelKey: 'string',
     valueType: 'string',
+    disabled: 'boolean'
   },
   events: {
     'input input' : 'changeInputHandler',
@@ -32,11 +33,12 @@ module.exports = AmpersandInputView.extend({
     AmpersandInputView.prototype.initialize.apply(this, arguments);
   },
   render: function () {
+    let disabled = this.disabled ? "disabled" : "";
     if(this.label) {
       this.template = [
         '<label>',
             '<span data-hook="label"></span>',
-            '<input class="form-input labeled">',
+            `<input class="form-input labeled" ${disabled}>`,
             '<div data-hook="message-container" class="message message-below message-error text-danger">',
                 '<p data-hook="message-text"></p>',
             '</div>',
@@ -45,7 +47,7 @@ module.exports = AmpersandInputView.extend({
     }else{
       this.template = [
         '<label>',
-            '<input class="form-input">',
+            `<input class="form-input" ${disabled}>`,
             '<div data-hook="message-container" class="message message-below message-error text-danger">',
                 '<p data-hook="message-text"></p>',
             '</div>',

From 462fb33c750a24f178f6d9831bd30bb4e6c5dfe1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:54:28 -0400
Subject: [PATCH 040/110] Added new properties for 'c' and 'rho' to domain type
 model.  Refactored the add type function to use spatialpy default instead of
 passing values as args.

---
 client/models/domain-type.js  |  8 +++++++-
 client/models/domain-types.js | 21 +++++++++++----------
 2 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/client/models/domain-type.js b/client/models/domain-type.js
index 930f6a197f..2d9536d0be 100644
--- a/client/models/domain-type.js
+++ b/client/models/domain-type.js
@@ -21,15 +21,21 @@ var State = require('ampersand-state');
 
 module.exports = State.extend({
   props: {
+    c: 'number',
     fixed: 'boolean',
     mass: 'number',
     name: 'string',
     nu: 'number',
+    rho: 'number',
     typeID: 'number',
     volume: 'number'
   },
   session: {
-    numParticles: 'number'
+    numParticles: 'number',
+    selected: {
+      type: 'boolean',
+      default: false
+    }
   },
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments)
diff --git a/client/models/domain-types.js b/client/models/domain-types.js
index 3d557a1dde..df5cf24b13 100644
--- a/client/models/domain-types.js
+++ b/client/models/domain-types.js
@@ -24,19 +24,20 @@ var Collection = require('ampersand-collection');
 module.exports = Collection.extend({
   model: Type,
   indexes: ['typeID'],
-  addType: function (vol, mass, nu, fixed, id=null) {
-    if(!id) {
-      id = this.parent.getDefaultTypeID();
-    }
+  addType: function () {
+    let id = this.parent.getDefaultTypeID();
     let name = String(id);
-    var type = new Type({
-        fixed: fixed,
-        mass: mass,
-        nu: nu,
-        typeID: id,
+    let type = new Type({
+        c: 10,
+        fixed: false,
+        mass: 1.0,
         name: name,
-        volume: vol
+        nu: 0.0,
+        rho: 1.0,
+        typeID: id,
+        volume: 1.0
     });
+    type.selected = true;
     this.add(type);
     return name;
   },

From b9e701d26808de0eac78d30f27143904b6fdfb20 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 07:59:05 -0400
Subject: [PATCH 041/110] Added new properties for 'c' and 'rho' to particle
 model.  Removed session properties.  Added function to compare the points of
 two particles.  Refactored the add particle function to allow it to accept a
 particle state in addition to property values.

---
 client/models/particle.js  | 13 +++++++++----
 client/models/particles.js | 26 ++++++++++++++++----------
 2 files changed, 25 insertions(+), 14 deletions(-)

diff --git a/client/models/particle.js b/client/models/particle.js
index 1871d36f2c..0a685631bf 100644
--- a/client/models/particle.js
+++ b/client/models/particle.js
@@ -21,21 +21,26 @@ var State = require('ampersand-state');
 
 module.exports = State.extend({
   props: {
+    c: 'number',
     fixed: 'boolean',
     mass: 'number',
     nu: 'number',
     particle_id: 'number',
     point: 'object',
+    rho: 'number',
     type: 'number',
     volume: 'number'
   },
-  session: {
-    pointChanged: 'boolean',
-    typeChanged: 'boolean'
-  },
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments)
   },
+  comparePoint(point) {
+    if(this.point.length !== point.length) { return false; }
+    for(var i = 0; i < this.point.length; i++) {
+      if(this.point[i] !== point[i]) { return false; }
+    }
+    return true;
+  },
   validate: function () {
     return true;
   }
diff --git a/client/models/particles.js b/client/models/particles.js
index 937f0000a7..968f1f6ff5 100644
--- a/client/models/particles.js
+++ b/client/models/particles.js
@@ -24,17 +24,23 @@ var Collection = require('ampersand-collection');
 module.exports = Collection.extend({
   model: Particle,
   indexes: ['particle_id'],
-  addParticle: function (point, vol, mass, type, nu, fixed) {
+  addParticle: function ({particle=null, point=[0,0,0], vol=1, mass=1, type=0, nu=0, fixed=false, c=10, rho=1}={}) {
     let id = this.parent.getDefaultID();
-    var particle = new Particle({
-        fixed: fixed,
-        mass: mass,
-        nu: nu,
-        particle_id: id,
-        point: point,
-        type: type,
-        volume: vol
-    });
+    if(particle) {
+      particle.particle_id = id;
+    }else{
+      particle = new Particle({
+          c: c,
+          fixed: fixed,
+          mass: mass,
+          nu: nu,
+          particle_id: id,
+          point: point,
+          rho: rho,
+          type: type,
+          volume: vol
+      });
+    }
     this.add(particle);
   },
   removeParticle: function (particle) {

From 5e9902f10d952cc1138bf0d4ad246a6a4aa92dd2 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 09:46:55 -0400
Subject: [PATCH 042/110] Removed old view and template files.

---
 client/templates/includes/edit3DDomain.pug | 103 ---------
 client/templates/includes/editParticle.pug |  63 ------
 client/views/edit-3D-domain.js             | 234 ---------------------
 client/views/edit-particle.js              | 210 ------------------
 4 files changed, 610 deletions(-)
 delete mode 100644 client/templates/includes/edit3DDomain.pug
 delete mode 100644 client/templates/includes/editParticle.pug
 delete mode 100644 client/views/edit-3D-domain.js
 delete mode 100644 client/views/edit-particle.js

diff --git a/client/templates/includes/edit3DDomain.pug b/client/templates/includes/edit3DDomain.pug
deleted file mode 100644
index 4a6e55b090..0000000000
--- a/client/templates/includes/edit3DDomain.pug
+++ /dev/null
@@ -1,103 +0,0 @@
-div.card.card-body
-
-  div
-
-    h4.mt-3 Particles Distribution
-
-    table.table
-      thead
-        tr
-          th(scope="col")
-          th(scope="col") X-Plane
-          th(scope="col") Y-Plane
-          th(scope="col") Z-Plane
-          th(scope="col") Total
-      tbody
-        tr
-          th(scope="row") Number of Particles
-          td: div(data-target="num-particles" data-hook="nx")
-          td: div(data-target="num-particles" data-hook="ny")
-          td: div(data-target="num-particles" data-hook="nz")
-          td: div(data-hook="total")
-
-  div
-
-    h4 Domain Limits
-
-    table.table
-      thead
-        tr
-          th(scope="col")
-          th(scope="col") X-Axis
-          th(scope="col") Y-Axis
-          th(scope="col") Z-Axis
-      tbody
-        tr
-          th(scope="row") Minimum
-          td: div(data-target="limits" data-hook="xLim-min")
-          td: div(data-target="limits" data-hook="yLim-min")
-          td: div(data-target="limits" data-hook="zLim-min")
-        tr
-          th(scope="row") Maximum
-          td: div(data-target="limits" data-hook="xLim-max")
-          td: div(data-target="limits" data-hook="yLim-max")
-          td: div(data-target="limits" data-hook="zLim-max")
-
-  div
-
-    h4.inline Advanced
-
-    button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#create-3D-domain-advanced", data-hook="collapse") +
-
-  div.collapse(id="create-3D-domain-advanced" data-hook="3D-domain-advanced-container")
-
-    div(data-hook="type-select")
-
-    h5 Type Defaults
-
-    table.table
-      thead
-        tr
-          th(scope="col") Mass
-          th(scope="col") Volume
-          th(scope="col") Viscosity
-          th(scope="col") Fixed
-
-      tbody
-        tr
-          td: div(data-hook="mass")
-          td: div(data-hook="volume")
-          td: div(data-hook="nu")
-          td: input(type="checkbox" data-hook="fixed" disabled)
-
-    h5 Particle Transformations
-
-    table.table
-      thead
-        tr
-          th(scope="col") X-Axis
-          th(scope="col") Y-Axis
-          th(scope="col") Z-Axis
-      tbody
-        tr
-          td: div(data-hook="domain-x-trans")
-          td: div(data-hook="domain-y-trans")
-          td: div(data-hook="domain-z-trans")
-
-  div.inline
-
-    button.btn.btn-outline-primary(data-hook="build-domain") Build Domain
-
-  div.mdl-edit-btn.saving-status.inline(data-hook="cd-in-progress")
-
-    div.spinner-grow.mr-2
-
-    span(data-hook="cd-action-in-progress")
-
-  div.mdl-edit-btn.saved-status.inline(data-hook="cd-complete")
-
-    span(data-hook="cd-action-complete")
-
-  div.mdl-edit-btn.save-error-status(data-hook="cd-error")
-
-    span(data-hook="cd-action-error")
diff --git a/client/templates/includes/editParticle.pug b/client/templates/includes/editParticle.pug
deleted file mode 100644
index c4b5d34153..0000000000
--- a/client/templates/includes/editParticle.pug
+++ /dev/null
@@ -1,63 +0,0 @@
-div.card.card-body
-
-  div.text-info.mb-4(data-hook="select-message-" + this.viewIndex style="display: none")
-    | Click on a particle in the Domain section to begin editing.
-
-  div
-
-    h4.inline.mr-2 Location:
-
-    div.inline.mr-2 (x:
-
-    div.inline.ml2(data-target="location" data-hook="x-coord-" + this.viewIndex)
-
-    div.inline.mr-2 ,  y:
-
-    div.inline.ml2(data-target="location" data-hook="y-coord-" + this.viewIndex)
-
-    div.inline.mr-2 ,  z:
-
-    div.inline.ml2(data-target="location" data-hook="z-coord-" + this.viewIndex)
-
-    div.inline )
-
-  h4 Particle Properties
-
-  table.table
-    thead
-      tr
-        th(scope="row") Type
-        th(scope="row") Mass
-        th(scope="row") Volume
-        th(scope="row") Viscosity
-        th(scope="row") Fixed
-
-    tbody
-      tr
-        td: div(data-target="type" data-hook="type-" + this.viewIndex)
-        td: div(data-target="mass" data-hook="mass-" + this.viewIndex)
-        td: div(data-target="volume" data-hook="volume-" + this.viewIndex)
-        td: div(data-target="nu" data-hook="nu-" + this.viewIndex)
-        td: input(type="checkbox" data-target="fixed" data-hook="fixed-" + this.viewIndex)
-
-  div
-
-    div.inline(data-hook="new-particle-btns-" + this.viewIndex)
-
-      button.btn.btn-outline-primary.box-shadow(data-hook="add-particle") Add Particle
-
-    div.inline(data-hook="edit-particle-btns-" + this.viewIndex)
-
-      button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="save-particle") Save Particle
-
-      button.btn.btn-outline-primary.box-shadow.ml-2(data-hook="remove-particle") Remove Particle
-
-    div.mdl-edit-btn.saving-status.inline(data-hook="ep-in-progress")
-
-      div.spinner-grow.mr-2
-
-      span(data-hook="ep-action-in-progress")
-
-    div.mdl-edit-btn.saved-status.inline(data-hook="ep-complete")
-
-      span(data-hook="ep-action-complete")
diff --git a/client/views/edit-3D-domain.js b/client/views/edit-3D-domain.js
deleted file mode 100644
index af6c0b404d..0000000000
--- a/client/views/edit-3D-domain.js
+++ /dev/null
@@ -1,234 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-var $ = require('jquery');
-var path = require('path');
-//support files
-var app = require('../app');
-var tests = require('./tests');
-//views
-var View = require('ampersand-view');
-var InputView = require('./input');
-var SelectView = require('ampersand-select-view');
-//templates
-var template = require('../templates/includes/edit3DDomain.pug');
-
-module.exports = View.extend({
-  template: template,
-  events: {
-    'change [data-target=num-particles]' : 'handleNumParticlesUpdate',
-    'change [data-target=limits]' : 'handleLimitsUpdate',
-    'change [data-hook=type-select]' : 'updateTypeAndDefaults',
-    'click [data-hook=build-domain]' : 'handleBuildDomain'
-  },
-  handleBuildDomain: function (e) {
-    this.startAction("Creating domain ...")
-    this.data.type = {"type_id":this.type.name, "mass":this.type.mass, "nu":this.type.nu, "fixed":this.type.fixed};
-    this.data.volume = this.type.volume;
-    let xtrans = Number($(this.queryByHook("domain-x-trans")).find('input')[0].value);
-    let ytrans = Number($(this.queryByHook("domain-y-trans")).find('input')[0].value);
-    let ztrans = Number($(this.queryByHook("domain-z-trans")).find('input')[0].value);
-    if(xtrans !== 0 || ytrans !== 0 || ztrans !== 0) {
-      this.data.transformation = [xtrans, ytrans, ztrans];
-    }
-    this.data.domainExists = Boolean(this.parent.plot);
-    let self = this;
-    let endpoint = path.join(app.getApiPath(), "spatial-model/3d-domain");
-    app.postXHR(endpoint, this.data, {
-      success: function (err, response, body) {
-        if(self.data.domainExists) {
-          self.parent.addParticles(body.particles);
-          if(self.parent.domain.x_lim[0] > body.limits.x_lim[0]) {
-            self.parent.domain.x_lim[0] = body.limits.x_lim[0];
-          }
-          if(self.parent.domain.y_lim[0] > body.limits.y_lim[0]) {
-            self.parent.domain.y_lim[0] = body.limits.y_lim[0];
-          }
-          if(self.parent.domain.z_lim[0] > body.limits.z_lim[0]) {
-            self.parent.domain.z_lim[0] = body.limits.z_lim[0];
-          }
-          if(self.parent.domain.x_lim[1] < body.limits.x_lim[1]) {
-            self.parent.domain.x_lim[1] = body.limits.x_lim[1];
-          }
-          if(self.parent.domain.y_lim[1] < body.limits.y_lim[1]) {
-            self.parent.domain.y_lim[1] = body.limits.y_lim[1];
-          }
-          if(self.parent.domain.z_lim[1] < body.limits.z_lim[1]) {
-            self.parent.domain.z_lim[1] = body.limits.z_lim[1];
-          }
-          self.parent.renderDomainLimitations();
-        }else{
-          self.parent.domain.x_lim = body.limits.x_lim;
-          self.parent.domain.y_lim = body.limits.y_lim;
-          self.parent.domain.z_lim = body.limits.z_lim;
-          body.particles.forEach((particle) => {
-            self.parent.domain.particles.addParticle(
-              particle.point, particle.volume, particle.mass, particle.type, particle.nu, particle.fixed
-            );
-          });
-          self.parent.plot = body.figure;
-          self.parent.renderDomainLimitations();
-          self.parent.displayDomain();
-        }
-        self.completeAction("Domain successfully created");
-        $('html, body').animate({
-            scrollTop: $("#domain-plot").offset().top
-        }, 20);
-      },
-      error: function (err, response, body) {
-        self.errorAction(body.Message);
-      }
-    });
-  },
-  handleLimitsUpdate: function (e) {
-    let data = e.target.parentElement.parentElement.dataset.hook.split("-");
-    let index = data[1] === "min" ? 0 : 1;
-    let value = Number(e.target.value);
-    this.data[data[0]][index] = value;
-  },
-  handleNumParticlesUpdate: function (e) {
-    let hook = e.target.parentElement.parentElement.dataset.hook;
-    let value = Number(e.target.value);
-    this.data[hook] = value;
-    this.updateTotalParticles();
-  },
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-    this.type = this.model.types.get(0, "typeID");
-    this.data = {"nx":1, "ny":1, "nz":1, "xLim":[0, 0],
-                 "yLim":[0, 0], "zLim":[0, 0], "type":0, "volume":1,
-                 "transformation": null}
-  },
-  render: function (attrs, options) {
-    View.prototype.render.apply(this, arguments);
-    this.renderNumberOfParticles();
-    this.updateTotalParticles();
-    this.renderParticleLimits();
-    this.renderType();
-    this.renderTypeDefaults();
-    this.renderDomainTransformations();
-  },
-  completeAction: function (action) {
-    $(this.queryByHook("cd-in-progress")).css("display", "none");
-    $(this.queryByHook("cd-action-complete")).text(action);
-    $(this.queryByHook("cd-complete")).css("display", "inline-block");
-    let self = this
-    setTimeout(function () {
-      $(self.queryByHook("cd-complete")).css("display", "none");
-    }, 5000);
-  },
-  errorAction: function (action) {
-    $(this.queryByHook("cd-in-progress")).css("display", "none");
-    $(this.queryByHook("cd-action-error")).text(action);
-    $(this.queryByHook("cd-error")).css("display", "block");
-    console.log(action)
-  },
-  renderDomainTransformations: function () {
-    let xtrans = new InputView({parent: this, required: true,
-                                name: 'x-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, xtrans, "domain-x-trans");
-    let ytrans = new InputView({parent: this, required: true,
-                                name: 'y-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, ytrans, "domain-y-trans");
-    let ztrans = new InputView({parent: this, required: true,
-                                name: 'z-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, ztrans, "domain-z-trans");
-  },
-  renderNumberOfParticles: function () {
-    let nxView = new InputView({parent: this, required: true,
-                                name: 'nx', valueType: 'number',
-                                tests: tests.valueTests,
-                                value: this.data.nx});
-    app.registerRenderSubview(this, nxView, "nx");
-    let nyView = new InputView({parent: this, required: true,
-                                name: 'ny', valueType: 'number',
-                                tests: tests.valueTests,
-                                value: this.data.ny});
-    app.registerRenderSubview(this, nyView, "ny");
-    let nzView = new InputView({parent: this, required: true,
-                                name: 'nz', valueType: 'number',
-                                tests: tests.valueTests,
-                                value: this.data.nz});
-    app.registerRenderSubview(this, nzView, "nz");
-  },
-  renderParticleLimits: function () {
-    let xLimMinView = new InputView({parent: this, required: true,
-                                name: 'x-lim-min', valueType: 'number',
-                                value: this.data.xLim[0]});
-    app.registerRenderSubview(this, xLimMinView, "xLim-min");
-    let yLimMinView = new InputView({parent: this, required: true,
-                                name: 'y-lim-min', valueType: 'number',
-                                value: this.data.yLim[0]});
-    app.registerRenderSubview(this, yLimMinView, "yLim-min");
-    let zLimMinView = new InputView({parent: this, required: true,
-                                name: 'z-lim-min', valueType: 'number',
-                                value: this.data.zLim[0]});
-    app.registerRenderSubview(this, zLimMinView, "zLim-min");
-    let xLimMaxView = new InputView({parent: this, required: true,
-                                name: 'x-lim-max', valueType: 'number',
-                                value: this.data.xLim[1]});
-    app.registerRenderSubview(this, xLimMaxView, "xLim-max");
-    let yLimMaxView = new InputView({parent: this, required: true,
-                                name: 'y-lim-max', valueType: 'number',
-                                value: this.data.yLim[1]});
-    app.registerRenderSubview(this, yLimMaxView, "yLim-max");
-    let zLimMaxView = new InputView({parent: this, required: true,
-                                name: 'z-lim-max', valueType: 'number',
-                                value: this.data.zLim[1]});
-    app.registerRenderSubview(this, zLimMaxView, "zLim-max");
-  },
-  renderType: function () {
-    var typeView = new SelectView({
-      label: 'Type:  ',
-      name: 'type',
-      required: true,
-      idAttribute: 'typeID',
-      textAttribute: 'name',
-      eagerValidate: true,
-      options: this.model.types,
-      value: this.type
-    });
-    app.registerRenderSubview(this, typeView, "type-select")
-  },
-  renderTypeDefaults: function () {
-    $(this.queryByHook("mass")).text(this.type.mass)
-    $(this.queryByHook("volume")).text(this.type.volume)
-    $(this.queryByHook("nu")).text(this.type.nu)
-    $(this.queryByHook("fixed")).prop("checked", this.type.fixed)
-  },
-  startAction: function (action) {
-    $(this.queryByHook("cd-complete")).css("display", "none");
-    $(this.queryByHook("cd-action-in-progress")).text(action);
-    $(this.queryByHook("cd-in-progress")).css("display", "inline-block");
-  },
-  update: function (e) {},
-  updateTotalParticles: function (e) {
-    let total = this.data.nx * this.data.ny * this.data.nz;
-    $(this.queryByHook("total")).text(total)
-    $(this.queryByHook("build-domain")).prop("disabled", total <= 0)
-  },
-  updateTypeAndDefaults: function (e) {
-    let id = Number(e.target.selectedOptions.item(0).value);
-    this.type = this.model.types.get(id, "typeID");
-    this.renderTypeDefaults();
-  },
-  updateValid: function (e) {}
-});
\ No newline at end of file
diff --git a/client/views/edit-particle.js b/client/views/edit-particle.js
deleted file mode 100644
index e28682ac34..0000000000
--- a/client/views/edit-particle.js
+++ /dev/null
@@ -1,210 +0,0 @@
-/*
-StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
-
-var $ = require('jquery');
-var _ = require('underscore');
-//support files
-let app = require('../app');
-var tests = require('../views/tests');
-//views
-var View = require('ampersand-view');
-var InputView = require('./input');
-var SelectView = require('ampersand-select-view');
-//templates
-var template = require('../templates/includes/editParticle.pug');
-
-module.exports = View.extend({
-  template: template,
-  events: {
-    'change [data-target=location]' : 'handleUpdateLocation',
-    'change [data-target=mass]' : 'handleUpdateMass',
-    'change [data-target=volume]' : 'handleUpdateVolume',
-    'change [data-target=nu]' : 'handleUpdateNu',
-    'change [data-target=fixed]' : 'handleUpdateFixed',
-    'change [data-target=type]' : 'handleUpdateType',
-    'click [data-hook=add-particle]' : 'handleAddParticle',
-    'click [data-hook=save-particle]' : 'handleSaveParticle',
-    'click [data-hook=remove-particle]' : 'handleRemoveParticle'
-  },
-  handleAddParticle: function (e) {
-    this.startAction("Adding particle ...")
-    this.parent.addParticle(this.model, {cb: _.bind(function () {
-      this.completeAction("Particle Added")
-    }, this)});
-  },
-  handleSaveParticle: function (e) {
-    this.startAction("Saving particle ...")
-    this.parent.updateParticle({cb: _.bind(function () {
-      this.completeAction("Particle Saved")
-    }, this)});
-  },
-  handleRemoveParticle: function (e) {
-    this.parent.deleteParticle();
-  },
-  handleUpdateFixed: function (e) {
-    let value = e.target.checked;
-    this.model.fixed = value;
-  },
-  handleUpdateLocation: function (e) {
-    let hook = e.target.parentElement.parentElement.dataset.hook;
-    let value = Number(e.target.value);
-    if(hook.startsWith('x')) {
-      this.model.point[0] = value;
-    }else if(hook.startsWith('y')) {
-      this.model.point[1] = value;
-    }else{
-      this.model.point[2] = value;
-    }
-    this.model.pointChanged = true;
-  },
-  handleUpdateMass: function (e) {
-    let value = Number(e.target.value);
-    this.model.mass = value;
-  },
-  handleUpdateNu: function (e) {
-    let value = Number(e.target.value);
-    this.model.nu = value;
-  },
-  handleUpdateType: function (e) {
-    let id = Number(e.target.selectedOptions.item(0).value);
-    let oldType = this.parent.domain.types.get(this.model.type, "typeID");
-    let newType = this.parent.domain.types.get(id, "typeID");
-    if(this.model.mass === oldType.mass) {
-      this.model.mass = newType.mass;
-    }
-    if(this.model.volume === oldType.volume) {
-      this.model.volume = newType.volume;
-    }
-    if(this.model.nu === oldType.nu) {
-      this.model.nu = newType.nu;
-    }
-    if(this.model.fixed === oldType.fixed) {
-      this.model.fixed = newType.fixed;
-    }
-    this.renderProperties();
-    this.model.type = id;
-    this.model.typeChanged = true;
-  },
-  handleUpdateVolume: function (e) {
-    let value = Number(e.target.value);
-    this.model.volume = value;
-  },
-  initialize: function (attrs, options) {
-    View.prototype.initialize.apply(this, arguments);
-    this.newParticle = attrs.newParticle;
-    this.viewIndex = this.newParticle ? 0 : 1;
-  },
-  completeAction: function (action) {
-    $(this.queryByHook("ep-in-progress")).css("display", "none");
-    $(this.queryByHook("ep-action-complete")).text(action);
-    $(this.queryByHook("ep-complete")).css("display", "inline-block");
-    console.log(action)
-    let self = this
-    setTimeout(function () {
-      $(self.queryByHook("ep-complete")).css("display", "none");
-    }, 5000);
-  },
-  disableAll: function () {
-    $(this.queryByHook("x-coord-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("y-coord-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("z-coord-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("type-" + this.viewIndex)).find('select').prop('disabled', true);
-    $(this.queryByHook("mass-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("volume-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("nu-" + this.viewIndex)).find('input').prop('disabled', true);
-    $(this.queryByHook("fixed-" + this.viewIndex)).prop('disabled', true);
-    $(this.queryByHook("save-particle")).prop('disabled', true);
-    $(this.queryByHook("remove-particle")).prop('disabled', true);
-  },
-  render: function (attrs, options) {
-    View.prototype.render.apply(this, arguments);
-    this.type = this.parent.domain.types.get(this.model.type, "typeID");
-    if(this.newParticle) {
-      $(this.queryByHook("edit-particle-btns-"+this.viewIndex)).css("display", "none");
-    }else{
-      $(this.queryByHook("new-particle-btns-"+this.viewIndex)).css("display", "none");
-    }
-    this.renderLocation();
-    this.renderProperties();
-    this.renderType();
-    if(!this.newParticle && !this.parent.actPart.part) {
-      $(this.queryByHook("select-message-" + this.viewIndex)).css('display', 'block')
-      this.disableAll();
-    }
-  },
-  renderLocation: function () {
-    var xCoord = new InputView({parent: this, required: true,
-                                name: 'x-coord', valueType: 'number',
-                                value: this.model.point[0] || 0});
-    app.registerRenderSubview(this, xCoord, "x-coord-" + this.viewIndex);
-    var yCoord = new InputView({parent: this, required: true,
-                                name: 'y-coord', valueType: 'number',
-                                value: this.model.point[1] || 0});
-    app.registerRenderSubview(this, yCoord, "y-coord-" + this.viewIndex);
-    var zCoord = new InputView({parent: this, required: true,
-                                name: 'z-coord', valueType: 'number',
-                                value: this.model.point[2] || 0});
-    app.registerRenderSubview(this, zCoord, "z-coord-" + this.viewIndex);
-  },
-  renderProperties: function () {
-    if(this.massView) {
-      this.massView.remove();
-    }
-    if(this.volView) {
-      this.volView.remove();
-    }
-    if(this.nuView) {
-      this.nuView.remove();
-    }
-    this.massView = new InputView({parent: this, required: true,
-                                  name: 'mass', valueType: 'number',
-                                  value: this.model.mass || this.type.mass});
-    app.registerRenderSubview(this, this.massView, "mass-" + this.viewIndex);
-    this.volView = new InputView({parent: this, required: true,
-                                 name: 'volume', valueType: 'number',
-                                 value: this.model.volume || this.type.volume});
-    app.registerRenderSubview(this, this.volView, "volume-" + this.viewIndex);
-    this.nuView = new InputView({parent: this, required: true,
-                                name: 'viscosity', valueType: 'number',
-                                value: this.model.nu || this.type.nu});
-    app.registerRenderSubview(this, this.nuView, "nu-" + this.viewIndex);
-    let fixed = this.model.fixed || this.type.fixed;
-    $(this.queryByHook("fixed-" + this.viewIndex)).prop("checked", fixed);
-  },
-  renderType: function () {
-    var typeView = new SelectView({
-      label: '',
-      name: 'type',
-      required: true,
-      idAttribute: 'typeID',
-      textAttribute: 'name',
-      eagerValidate: true,
-      options: this.parent.domain.types,
-      value: this.parent.domain.types.get(this.model.type, "typeID")
-    });
-    app.registerRenderSubview(this, typeView, "type-" + this.viewIndex)
-  },
-  startAction: function (action) {
-    $(this.queryByHook("ep-complete")).css("display", "none");
-    $(this.queryByHook("ep-action-in-progress")).text(action);
-    $(this.queryByHook("ep-in-progress")).css("display", "inline-block");
-    console.log(action)
-  },
-  update: function (e) {},
-  updateValid: function (e) {}
-});
\ No newline at end of file

From cb4436cb5c51d197840fb993c4ec1a35896703cd Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 09:48:04 -0400
Subject: [PATCH 043/110] Removed the plot from the response of the create 3D
 domain api request.

---
 client/domain-view/domain-view.js               | 5 +----
 client/domain-view/views/edit-3D-domain-view.js | 2 +-
 stochss/handlers/util/stochss_spatial_model.py  | 3 ---
 3 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index 90d6743eba..ee2d3a1767 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -79,10 +79,7 @@ module.exports = View.extend({
       this.displayFigure();
     }});
   },
-  add3DDomain: function (limits, particles, plot) {
-    if(plot) {
-      this.plot = plot;
-    }
+  add3DDomain: function (limits, particles) {
     let limitsChanged = this.changeDomainLimits(limits, Boolean(plot));
     particles.forEach((particle) => {
       particle = new Particle(particle);
diff --git a/client/domain-view/views/edit-3D-domain-view.js b/client/domain-view/views/edit-3D-domain-view.js
index d1f1f585b1..cfd4c503b4 100644
--- a/client/domain-view/views/edit-3D-domain-view.js
+++ b/client/domain-view/views/edit-3D-domain-view.js
@@ -81,7 +81,7 @@ module.exports = View.extend({
     let endpoint = path.join(app.getApiPath(), "spatial-model/3d-domain");
     app.postXHR(endpoint, this.data, {
       success: (err, response, body) => {
-        this.parent.add3DDomain(body.limits, body.particles, body.figure);
+        this.parent.add3DDomain(body.limits, body.particles);
         this.completeAction();
         $('html, body').animate({
             scrollTop: $("#domain-figure").offset().top
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 914424dc65..c7de6e5f4a 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -593,9 +593,6 @@ def get_particles_from_3d_domain(self, data):
         domain = self.__build_stochss_domain(s_domain=s_domain, data=data)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
         resp = {"particles":domain['particles'], "limits":limits}
-        if data['domainExists']:
-            return resp
-        resp['figure'] = json.loads(self.get_domain_plot(domains=(s_domain, domain))[0])
         return resp
 
 

From 8f70aabc9e712fb983c838fa5e06c395cdc92797 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 09:53:35 -0400
Subject: [PATCH 044/110] Refactored the domain editor page to use the new
 domain view.

---
 client/pages/domain-editor.js           | 851 +++---------------------
 client/templates/pages/domainEditor.pug | 282 +-------
 2 files changed, 88 insertions(+), 1045 deletions(-)

diff --git a/client/pages/domain-editor.js b/client/pages/domain-editor.js
index c85940e474..530612da2a 100644
--- a/client/pages/domain-editor.js
+++ b/client/pages/domain-editor.js
@@ -16,225 +16,35 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
-var $ = require('jquery');
+let $ = require('jquery');
 let path = require('path');
-var _ = require('underscore');
 //support files
-var app = require('../app');
-var tests = require('../views/tests');
-var Plotly = require('../lib/plotly');
-var Tooltips = require('../tooltips');
+let app = require('../app');
 let modals = require('../modals');
-//views
-var PageView = require('../pages/base');
-var InputView = require('../views/input');
-var SelectView = require('ampersand-select-view');
-var ParticleView = require('../views/edit-particle');
-var EditDomainTypeView = require('../views/edit-domain-type');
-var Create3DDomainView = require('../views/edit-3D-domain');
-//collections
-var Collection = require('ampersand-collection');
 //models
-var Model = require('../models/model');
-var Domain = require('../models/domain');
-var Particle = require('../models/particle');
-var TypeModel = require('../models/domain-type');
+let Model = require('../models/model');
+let Domain = require('../models/domain');
+//views
+let DomainView = require('../domain-view/domain-view');
+let PageView = require('../pages/base');
 //templates
-var template = require('../templates/pages/domainEditor.pug');
+let template = require('../templates/pages/domainEditor.pug');
 
 import initPage from './page.js';
 
 let DomainEditor = PageView.extend({
   template: template,
   events: {
-    'click [data-toggle=collapse]' : 'changeCollapseButtonText',
-    'click [data-hook=add-domain-type]' : 'handleAddDomainType',
-    'click [data-hook=set-type-defaults]' : 'handleSetDefaults',
     'click [data-hook=save-to-model]' : 'handleSaveToModel',
     'click [data-hook=save-to-file]' : 'handleSaveToFile',
-    'click [data-hook=import-particles-btn]' : 'handleImportMesh',
-    'click [data-hook=set-particle-types-btn]' : 'getTypesFromFile',
-    'change [data-hook=static-domain]' : 'setStaticDomain',
-    'change [data-hook=density]' : 'setDensity',
-    'change [data-target=gravity]' : 'setGravity',
-    'change [data-hook=pressure]' : 'setPressure',
-    'change [data-hook=speed]' : 'setSpeed',
-    'change [data-name=limitation]' : 'setLimitation',
-    'change [data-target=reflect]' : 'setBoundaryCondition',
-    'change #meshfile' : 'updateImportBtn',
-    'change [data-hook=mesh-type-select]' : 'updateMeshTypeAndDefaults',
-    'change [data-hook=types-file-select]' : 'handleSelectTypeFile',
-    'change [data-hook=types-file-location-select]' : 'handleSelectTypeLocation'
-  },
-  handleAddDomainType: function () {
-    this.selectedType = "new";
-    this.renderEditTypeDefaults();
-  },
-  handleImportMesh: function (e) {
-    this.startAction("Importing mesh ...", "im")
-    let data = {"type":null, "transformation":null}
-    let id = Number($(this.queryByHook("mesh-type-select")).find('select')[0].value)
-    if(id > 0) {
-      data.type = this.domain.types.get(id, "typeID").toJSON();
-    }
-    let xTrans = Number($(this.queryByHook("mesh-x-trans")).find('input')[0].value)
-    let yTrans = Number($(this.queryByHook("mesh-y-trans")).find('input')[0].value)
-    let zTrans = Number($(this.queryByHook("mesh-z-trans")).find('input')[0].value)
-    if(xTrans !== 0 || yTrans !== 0 || zTrans !== 0) {
-      data.transformation = [xTrans, yTrans, zTrans];
-    }
-    this.importMesh(data)
-  },
-  importMesh: function (data) {
-    let self = this;
-    let file = $("#meshfile").prop("files")[0];
-    let typeFiles = $("#typefile").prop("files")
-    let formData = new FormData();
-    formData.append("datafile", file);
-    formData.append("particleData", JSON.stringify(data));
-    if(typeFiles.length) {
-      formData.append("typefile", typeFiles[0]);
-    }
-    let endpoint = path.join(app.getApiPath(), 'spatial-model/import-mesh');
-    app.postXHR(endpoint, formData, {
-      success: function (err, response, body) {
-        body = JSON.parse(body);
-        if(body.types) {
-          self.addMissingTypes(body.types)
-        }
-        self.addParticles(body.particles);
-        if(self.domain.x_lim[0] > body.limits.x_lim[0]) {
-          self.domain.x_lim[0] = body.limits.x_lim[0]
-        }
-        if(self.domain.y_lim[0] > body.limits.y_lim[0]) {
-          self.domain.y_lim[0] = body.limits.y_lim[0]
-        }
-        if(self.domain.z_lim[0] > body.limits.z_lim[0]) {
-          self.domain.z_lim[0] = body.limits.z_lim[0]
-        }
-        if(self.domain.x_lim[1] < body.limits.x_lim[1]) {
-          self.domain.x_lim[1] = body.limits.x_lim[1]
-        }
-        if(self.domain.y_lim[1] < body.limits.y_lim[1]) {
-          self.domain.y_lim[1] = body.limits.y_lim[1]
-        }
-        if(self.domain.z_lim[1] < body.limits.z_lim[1]) {
-          self.domain.z_lim[1] = body.limits.z_lim[1]
-        }
-        self.renderDomainLimitations();
-        self.completeAction("Mesh successfully imported", "im")
-        $('html, body').animate({
-            scrollTop: $("#domain-plot").offset().top
-        }, 20);
-      },
-      error: function (err, response, body) {
-        body = JSON.parse(body);
-        self.errorAction(body.Message, "im")
-      }
-    }, false)
-  },
-  handleSetDefaults: function (e) {
-    let mass = Number($(this.queryByHook("td-mass")).find('input')[0].value);
-    let vol = Number($(this.queryByHook("td-vol")).find('input')[0].value);
-    let nu = Number($(this.queryByHook("td-nu")).find('input')[0].value);
-    let fixed = $(this.queryByHook("td-fixed")).prop("checked");
-    if(this.selectedType === "new") {
-      let name = this.domain.types.addType(vol, mass, nu, fixed)
-      if(this.domain.particles.length > 0) {
-        this.addType(name);
-      }
-    }else{
-      let type = this.domain.types.get(this.selectedType, "typeID")
-      type.mass = mass;
-      type.volume = vol;
-      type.nu = nu;
-      type.fixed = fixed;
-    }
-    this.renderDomainTypes();
-    $(this.queryByHook("edit-defaults")).css("display", "none");
-  },
-  handleSaveToModel: function () {
-    if(this.model) {
-      this.startAction("Saving domain to model ...", "sd");
-      this.model.domain = this.domain;
-      this.model.saveModel(_.bind(function () {
-        this.completeAction("Domain saved to model", "sd");
-      }, this));
-      window.location.replace(this.getBreadcrumbData().model.href);
-    }
-  },
-  handleSaveToFile: function () {
-    this.startAction("Saving the domain to file (.domn) ...", "sd")
-    if(this.domain.directory && !this.domain.dirname) {
-      this.saveDomain()
-    }else{
-      var self = this
-      if(document.querySelector('#newDomainModal')) {
-        document.querySelector('#newDomainModal').remove()
-      }
-      let modal = $(modals.createDomainHtml()).modal();
-      let okBtn = document.querySelector('#newDomainModal .ok-model-btn');
-      let input = document.querySelector('#newDomainModal #domainNameInput');
-      input.addEventListener("keyup", function (event) {
-        if(event.keyCode === 13){
-          event.preventDefault();
-          okBtn.click();
-        }
-      });
-      input.addEventListener("input", function (e) {
-        var endErrMsg = document.querySelector('#newDomainModal #domainNameInputEndCharError')
-        var charErrMsg = document.querySelector('#newDomainModal #domainNameInputSpecCharError')
-        let error = app.validateName(input.value)
-        okBtn.disabled = error !== "" || input.value.trim() === ""
-        charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
-        endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
-      });
-      okBtn.addEventListener('click', function (e) {
-        if (Boolean(input.value)) {
-          modal.modal('hide')
-          let name = input.value.trim()
-          self.saveDomain(name);
-        }
-      });
-    }
-  },
-  handleSelectTypeFile: function (e) {
-    let value = e.srcElement.value;
-    if(value) {
-      if(this.typeDescriptions[value].length <= 1) {
-        $(this.queryByHook("type-location-message")).css('display', "none");
-        $(this.queryByHook("type-location-container")).css("display", "none");
-        this.typeDescriptionsFile = this.typeDescriptions[value][0];
-        var disabled = false;
-      }else{
-        $(this.queryByHook("type-location-message")).css('display', "block");
-        $(this.queryByHook("type-location-container")).css("display", "inline-block");
-        this.renderTypesLocationSelect(this.typeDescriptions[value]);
-        var disabled = true;
-      }
-    }else{
-      $(this.queryByHook("type-location-message")).css('display', "none");
-      $(this.queryByHook("type-location-container")).css("display", "none");
-      var disabled = true;
-    }
-    $(this.queryByHook("set-particle-types-btn")).prop("disabled", disabled);
-  },
-  handleSelectTypeLocation: function (e) {
-    this.typeDescriptionsFile = e.srcElement.value;
-    $(this.queryByHook("set-particle-types-btn")).prop("disabled", false);
-  },
-  updateImportBtn: function (e) {
-    $(this.queryByHook("import-particles-btn")).prop("disabled", !Boolean(e.target.files.length))
   },
   initialize: function (attrs, options) {
     PageView.prototype.initialize.apply(this, arguments);
-    this.tooltips = Tooltips.domainEditor;
-    var self = this;
     let urlParams = new URLSearchParams(window.location.search)
     let modelPath = urlParams.has("path") ? urlParams.get("path") : null;
     let domainPath = urlParams.has("domainPath") ? urlParams.get("domainPath") : null;
     let newDomain = urlParams.has("new") ? true : false;
-    this.queryStr = modelPath ? "?path=" + modelPath : "?"
+    this.queryStr = modelPath ? `?path=${modelPath}` : "?"
     if(newDomain) {
       if(modelPath) {
         this.queryStr += "&"
@@ -248,186 +58,40 @@ let DomainEditor = PageView.extend({
     }
     let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + this.queryStr
     app.getXHR(endpoint, {
-      success: function (err, response, body) {
-        self.domain = new Domain(body.domain);
-        self.domain.directory = domainPath
-        self.domain.dirname = newDomain && !modelPath ? domainPath : null
-        self.model = self.buildModel(body.model, modelPath);
-        self.actPart = {"part":null, "tn":0, "pn":0};
-        self.renderSubviews();
-      }
-    });
-    $(document).on('shown.bs.modal', function (e) {
-      $('[autofocus]', e.target).focus();
-    });
-  },
-  addParticle: function (newPart, {fromImport=false, cb=null}={}) {
-    this.domain.particles.addParticle(newPart.point, newPart.volume,
-                                      newPart.mass, newPart.type,
-                                      newPart.nu, newPart.fixed);
-    let numPart = this.domain.particles.models.length
-    let particle = this.domain.particles.models[numPart-1]
-    this.plot.data[particle.type].ids.push(particle.particle_id);
-    this.plot.data[particle.type].x.push(particle.point[0]);
-    this.plot.data[particle.type].y.push(particle.point[1]);
-    this.plot.data[particle.type].z.push(particle.point[2]);
-    if(!fromImport) {
-      this.renderDomainTypes();
-      this.updatePlot();
-    }
-    if(cb) {
-      cb();
-    }
-  },
-  addParticles: function (particles) {
-    let self = this;
-    particles.forEach(function (particle) {
-      self.addParticle(particle, {fromImport: true});
-    });
-    this.renderDomainTypes();
-    this.updatePlot();
-  },
-  addMissingTypes: function (types) {
-    let self = this;
-    let defaultType = self.domain.types.get(0, "typeID");
-    types.forEach(function (type) {
-      let domainType = self.domain.types.get(type, "typeID");
-      if(!domainType) {
-        self.domain.types.addType(defaultType.volume, defaultType.mass,
-                                  defaultType.nu, defaultType.fixed, type);
-        self.addType(String(type));
+      success: (err, response, body) => {
+        this.domain = new Domain(body.domain);
+        this.domain.directory = domainPath
+        this.domain.dirname = newDomain && !modelPath ? domainPath : null
+        this.model = this.buildModel(body.model, modelPath);
+        this.renderSubviews();
       }
     });
   },
-  addType: function (name) {
-    this.renderEditParticle();
-    this.renderNewParticle();
-    var trace = {"ids":[], "x":[], "y":[], "z":[], "name":name};
-    trace['marker'] = this.plot.data[0].marker;
-    trace['mode'] = this.plot.data[0].mode;
-    trace['type'] = this.plot.data[0].type;
-    this.plot.data.push(trace)
-    this.updatePlot()
-  },
   buildModel: function (modelData, modelPath) {
     if(!modelPath) {
       return null;
     }
-    var model = new Model(modelData);
+    let model = new Model(modelData);
     model.for = "domain";
     model.isPreview = false;
     model.directory = modelPath;
     return model;
   },
-  changeCollapseButtonText: function (e) {
-    app.changeCollapseButtonText(this, e);
-  },
-  changeParticleLocation: function (x, y, z) {
-    this.domain.particles.get(this.actPart.part.particle_id, "particle_id").point = [x, y, z];
-    this.plot.data[this.actPart.tn].x[this.actPart.pn] = x;
-    this.plot.data[this.actPart.tn].y[this.actPart.pn] = y;
-    this.plot.data[this.actPart.tn].z[this.actPart.pn] = z;
-    this.actPart.part.pointChanged = false;
-  },
-  changeParticleTypes: function (types) {
-    let self = this;
-    types.forEach(function (type) {
-      let particle = self.domain.particles.get(type.particle_id, "particle_id");
-      self.actPart.part = particle;
-      for(var i = 0; i < self.plot.data.length; i++) {
-        let trace = self.plot.data[i];
-        if(trace.ids.includes(String(type.particle_id))){
-          self.actPart.tn = self.plot.data.indexOf(trace);
-          self.actPart.pn = trace.ids.indexOf(String(type.particle_id));
-          break;
-        }
-      };
-      self.changeParticleType(type.typeID)
-    });
-    this.renderDomainTypes();
-    this.updatePlot();
-  },
-  changeParticleType: function (type) {
-    this.domain.particles.get(this.actPart.part.particle_id, "particle_id").type = type
-    let id = this.plot.data[this.actPart.tn].ids.splice(this.actPart.pn, 1)[0];
-    let x = this.plot.data[this.actPart.tn].x.splice(this.actPart.pn, 1)[0];
-    let y = this.plot.data[this.actPart.tn].y.splice(this.actPart.pn, 1)[0];
-    let z = this.plot.data[this.actPart.tn].z.splice(this.actPart.pn, 1)[0];
-    this.plot.data[type].ids.push(id);
-    this.plot.data[type].x.push(x);
-    this.plot.data[type].y.push(y);
-    this.plot.data[type].z.push(z);
-    this.actPart.part.typeChanged = false;
-  },
-  completeAction: function (action, src) {
-    $(this.queryByHook(src + "-in-progress")).css("display", "none");
-    $(this.queryByHook(src + "-action-complete")).text(action);
-    $(this.queryByHook(src + "-complete")).css("display", "inline-block");
-    console.log(action)
-    let self = this
-    setTimeout(function () {
-      $(self.queryByHook(src + "-complete")).css("display", "none");
+  completeAction: function (action) {
+    $(this.queryByHook("sd-in-progress")).css("display", "none");
+    $(this.queryByHook("sd-action-complete")).text(action);
+    $(this.queryByHook("sd-complete")).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook("sd-complete")).css("display", "none");
     }, 5000);
   },
-  deleteParticle: function () {
-    this.domain.particles.removeParticle(this.actPart.part);
-    this.plot.data[this.actPart.tn].ids.splice(this.actPart.pn, 1);
-    this.plot.data[this.actPart.tn].x.splice(this.actPart.pn, 1);
-    this.plot.data[this.actPart.tn].y.splice(this.actPart.pn, 1);
-    this.plot.data[this.actPart.tn].z.splice(this.actPart.pn, 1);
-    this.actPart.part = null;
-    this.updatePlot();
-    this.renderEditParticle();
-    this.renderDomainTypes();
-    $('html, body').animate({
-        scrollTop: $("#domain-plot").offset().top
-    }, 20);
-  },
-  deleteType: function (typeID) {
-    if(this.actPart.part && this.actPart.part.type >= typeID) {
-      this.actPart.part = null;
-    }
-    this.unassignAllParticles(typeID, false);
-    let type = this.domain.types.get(typeID, "typeID");
-    this.domain.types.removeType(type);
-    this.renderEditParticle();
-    this.renderNewParticle();
-    this.plot.data.splice(typeID, 1);
-    this.updatePlot();
-  },
-  deleteTypeAndParticles: function (typeID) {
-    if(this.actPart.part && this.actPart.part.type >= typeID) {
-      this.actPart.part = null;
-    }
-    let self = this;
-    let particles = this.domain.particles.filter(function (particle) {
-      return particle.type === typeID;
-    });
-    this.domain.particles.removeParticles(particles);
-    let type = this.domain.types.get(typeID, "typeID");
-    this.domain.types.removeType(type);
-    this.renderEditParticle();
-    this.renderNewParticle();
-    this.plot.data.splice(typeID, 1);
-    this.updatePlot();
-  },
-  displayDomain: function () {
-    if(!this.plot) {
-      return
-    }
-    $(this.queryByHook("domain-plot-empty")).css('display', 'none');
-    var el = this.queryByHook("domain-plot");
-    Plotly.newPlot(el, this.plot);
-    el.on('plotly_click', _.bind(this.selectParticle, this));
-  },
-  errorAction: function (action, src) {
-    $(this.queryByHook(src + "-in-progress")).css("display", "none");
-    $(this.queryByHook(src + "-action-error")).text(action);
-    $(this.queryByHook(src + "-error")).css("display", "block");
-    console.log(action)
+  errorAction: function (action) {
+    $(this.queryByHook("sd-in-progress")).css("display", "none");
+    $(this.queryByHook("sd-action-error")).text(action);
+    $(this.queryByHook("sd-error")).css("display", "block");
   },
   getBreadcrumbData: function () {
-    var data = {"project":null, "model":null};
+    let data = {"project":null, "model":null};
     var projEP = "stochss/project/manager?path="
     var mdlEP = "stochss/models/edit?path="
     if(this.model) {
@@ -455,217 +119,59 @@ let DomainEditor = PageView.extend({
     }
     return data
   },
-  getNewParticle: function () {
-    var particle = new Particle({
-      point: [0, 0, 0],
-      mass: 1.0,
-      volume: 1.0,
-      nu: 0.0,
-      fixed: false,
-      type: 0
-    });
-    return particle;
-  },
-  getTypesFromFile: function (typePath) {
-    this.startAction("Setting types ...", "st")
-    let self = this;
-    let queryStr = "?path=" + this.typeDescriptionsFile;
-    let endpoint = path.join(app.getApiPath(), "spatial-model/particle-types") + queryStr;
-    app.getXHR(endpoint, {
-      success: function (err, response, body) {
-        self.addMissingTypes(body.names);
-        self.changeParticleTypes(body.types);
-        self.completeAction("Types set", "st");
-      },
-      error: function (err, response, body) {
-        self.errorAction(body.Message, "st");
-        console.log(err);
-      }
-    });
-  },
-  renameType: function (index, newName) {
-    this.domain.types.get(index, "typeID").name = newName;
-    this.renderEditParticle();
-    this.renderNewParticle();
-    this.renderTypeSelectView();
-    this.renderCreate3DDomain();
-    this.plot.data[index].name = newName;
-    this.updatePlot();
-  },
-  renderCreate3DDomain: function () {
-    if(this.create3DDomainView) {
-      this.create3DDomainView.remove()
-    }
-    this.create3DDomainView = new Create3DDomainView({
-      parent: this,
-      model: this.domain
-    });
-    app.registerRenderSubview(this, this.create3DDomainView, "add-3d-domain");
-  },
-  renderDomainLimitations: function () {
-    if(this.xLimMinView) {
-      this.xLimMinView.remove();
-      this.yLimMinView.remove();
-      this.zLimMinView.remove();
-      this.xLimMaxView.remove();
-      this.yLimMaxView.remove();
-      this.zLimMaxView.remove();
-    }
-    this.xLimMinView = new InputView({parent: this, required: true,
-                                     name: 'x-lim-min', valueType: 'number',
-                                     value: this.domain.x_lim[0] || 0});
-    app.registerRenderSubview(this, this.xLimMinView, "x_lim-min");
-    this.yLimMinView = new InputView({parent: this, required: true,
-                                     name: 'y-lim-min', valueType: 'number',
-                                     value: this.domain.y_lim[0] || 0});
-    app.registerRenderSubview(this, this.yLimMinView, "y_lim-min");
-    this.zLimMinView = new InputView({parent: this, required: true,
-                                     name: 'z-lim-min', valueType: 'number',
-                                     value: this.domain.z_lim[0] || 0});
-    app.registerRenderSubview(this, this.zLimMinView, "z_lim-min");
-    this.xLimMaxView = new InputView({parent: this, required: true,
-                                     name: 'x-lim-max', valueType: 'number',
-                                     value: this.domain.x_lim[1] || 0});
-    app.registerRenderSubview(this, this.xLimMaxView, "x_lim-max");
-    this.yLimMaxView = new InputView({parent: this, required: true,
-                                     name: 'y-lim-max', valueType: 'number',
-                                     value: this.domain.y_lim[1] || 0});
-    app.registerRenderSubview(this, this.yLimMaxView, "y_lim-max");
-    this.zLimMaxView = new InputView({parent: this, required: true,
-                                     name: 'z-lim-max', valueType: 'number',
-                                     value: this.domain.z_lim[1] || 0});
-    app.registerRenderSubview(this, this.zLimMaxView, "z_lim-max");
-  },
-  renderDomainProperties: function () {
-    $(this.queryByHook("static-domain")).prop("checked", this.domain.static);
-    let densityView = new InputView({parent: this, required: true,
-                                     name: 'density', valueType: 'number',
-                                     value: this.domain.rho_0 || 1});
-    app.registerRenderSubview(this, densityView, "density");
-    let gravityXView = new InputView({parent: this, required: true,
-                                     name: 'gravity-x', valueType: 'number',
-                                     value: this.domain.gravity[0], label: "X:  "});
-    app.registerRenderSubview(this, gravityXView, "gravity-x");
-    let gravityYView = new InputView({parent: this, required: true,
-                                     name: 'gravity-y', valueType: 'number',
-                                     value: this.domain.gravity[1], label: "Y:  "});
-    app.registerRenderSubview(this, gravityYView, "gravity-y");
-    let gravityZView = new InputView({parent: this, required: true,
-                                     name: 'gravity-z', valueType: 'number',
-                                     value: this.domain.gravity[2], label: "Z:  "});
-    app.registerRenderSubview(this, gravityZView, "gravity-z");
-    let pressureView = new InputView({parent: this, required: true,
-                                      name: 'pressure', valueType: 'number',
-                                      value: this.domain.p_0 || 0});
-    app.registerRenderSubview(this, pressureView, "pressure");
-    let speedView = new InputView({parent: this, required: true,
-                                   name: 'speed', valueType: 'number', 
-                                   value: this.domain.c_0 || 0});
-    app.registerRenderSubview(this, speedView, "speed");
-  },
-  renderDomainTypes: function () {
-    if(this.domainTypesView) {
-      this.domainTypesView.remove();
-      this.domain.types.forEach(function (type) {
-        type.numParticles = 0;
+  handleSaveToModel: function () {
+    if(this.model) {
+      this.startAction("Saving domain to model ...");
+      this.model.domain = this.domain;
+      this.model.saveModel(() => {
+        this.completeAction("Domain saved to model");
       });
+      window.location.replace(this.getBreadcrumbData().model.href);
     }
-    let self = this;
-    this.domain.particles.forEach(function (particle) {
-      self.domain.types.get(particle.type, "typeID").numParticles += 1;
-    });
-    let unaPart = "Number of Un-Assigned Particles: " + this.domain.types.get(0, "typeID").numParticles;
-    $(this.queryByHook("unassigned-particles")).text(unaPart);
-    this.domainTypesView = this.renderCollection(
-      this.domain.types,
-      EditDomainTypeView,
-      this.queryByHook("domain-types-list"),
-      {"filter": function (model) {
-        return model.typeID != 0;
-      }}
-    );
-    this.toggleDomainError()
-  },
-  renderEditTypeDefaults: function () {
-    if(this.massView) {
-      this.massView.remove();
-    }
-    if(this.volView) {
-      this.volView.remove();
-    }
-    if(this.nuView) {
-      this.nuView.remove();
-    }
-    var title = "Defaults for ";
-    if(this.selectedType === "new"){
-      var type = this.domain.types.get(0, "typeID")
-      title += "New Type";
-    }else{
-      var type = this.domain.types.get(this.selectedType, "typeID")
-      title += type.name
-    }
-    $(this.queryByHook("set-type-defaults-header")).text(title)
-    this.massView = new InputView({parent: this, required: true,
-                                  name: 'mass', valueType: 'number',
-                                  value: type.mass});
-    app.registerRenderSubview(this, this.massView, "td-mass");
-    this.volView = new InputView({parent: this, required: true,
-                                 name: 'volume', valueType: 'number',
-                                 value: type.volume});
-    app.registerRenderSubview(this, this.volView, "td-vol");
-    this.nuView = new InputView({parent: this, required: true,
-                                name: 'viscosity', valueType: 'number',
-                                value: type.nu});
-    app.registerRenderSubview(this, this.nuView, "td-nu");
-    $(this.queryByHook("td-fixed")).prop("checked", type.fixed);
-    $(this.queryByHook("edit-defaults")).css("display", "block");
   },
-  renderEditParticle: function () {
-    if(this.editParticleView) {
-      this.editParticleView.remove();
-    }
-    if(this.actPart.part) {
-      var particle = this.actPart.part;
+  handleSaveToFile: function () {
+    this.startAction("Saving the domain to file (.domn) ...")
+    if(this.domain.directory && !this.domain.dirname) {
+      this.saveDomain()
     }else{
-      var particle = this.getNewParticle();
+      if(document.querySelector('#newDomainModal')) {
+        document.querySelector('#newDomainModal').remove()
+      }
+      let modal = $(modals.createDomainHtml()).modal();
+      let okBtn = document.querySelector('#newDomainModal .ok-model-btn');
+      let input = document.querySelector('#newDomainModal #domainNameInput');
+      input.addEventListener("keyup", (event) => {
+        if(event.keyCode === 13){
+          event.preventDefault();
+          okBtn.click();
+        }
+      });
+      input.addEventListener("input", (e) => {
+        let endErrMsg = document.querySelector('#newDomainModal #domainNameInputEndCharError')
+        let charErrMsg = document.querySelector('#newDomainModal #domainNameInputSpecCharError')
+        let error = app.validateName(input.value)
+        okBtn.disabled = error !== "" || input.value.trim() === ""
+        charErrMsg.style.display = error === "both" || error === "special" ? "block" : "none"
+        endErrMsg.style.display = error === "both" || error === "forward" ? "block" : "none"
+      });
+      okBtn.addEventListener('click', (e) => {
+        if (Boolean(input.value)) {
+          modal.modal('hide')
+          let name = input.value.trim()
+          this.saveDomain({name: name});
+        }
+      });
     }
-    this.editParticleView = new ParticleView({
-      model: particle,
-      newParticle: false,
-    });
-    app.registerRenderSubview(this, this.editParticleView, "edit-particle");
-  },
-  renderMeshTransformations: function () {
-    let xtrans = new InputView({parent: this, required: true,
-                                name: 'x-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, xtrans, "mesh-x-trans");
-    let ytrans = new InputView({parent: this, required: true,
-                                name: 'y-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, ytrans, "mesh-y-trans");
-    let ztrans = new InputView({parent: this, required: true,
-                                name: 'z-transformation', valueType: 'number',
-                                value: 0});
-    app.registerRenderSubview(this, ztrans, "mesh-z-trans");
   },
-  renderMeshTypeDefaults: function (id) {
-    let type = this.domain.types.get(id, "typeID")
-    $(this.queryByHook("mesh-mass")).text(type.mass);
-    $(this.queryByHook("mesh-volume")).text(type.volume);
-    $(this.queryByHook("mesh-nu")).text(type.nu);
-    $(this.queryByHook("mesh-fixed")).prop("checked", type.fixed);
-  },
-  renderNewParticle: function () {
-    if(this.newParticleView) {
-      this.newParticleView.remove();
+  renderDomainView: function () {
+    if(this.doaminView) {
+      this.domainView.remove();
     }
-    var particle = this.getNewParticle();
-    this.newParticleView = new ParticleView({
-      model: particle,
-      newParticle: true,
+    this.domainView = new DomainView({
+      model: this.domain,
+      queryStr: this.queryStr
     });
-    app.registerRenderSubview(this, this.newParticleView, "new-particle");
+    app.registerRenderSubview(this, this.domainView, "domain-view-container");
   },
   renderSubviews: function () {
     let breadData = this.getBreadcrumbData();
@@ -697,220 +203,37 @@ let DomainEditor = PageView.extend({
       $(this.queryByHook("return-to-model")).css("display", "none");
       $(this.queryByHook("return-to-project")).css("display", "none");
     }
-    this.renderDomainProperties();
-    this.renderDomainLimitations();
-    $(this.queryByHook("reflect_x")).prop("checked", this.domain.boundary_condition.reflect_x);
-    $(this.queryByHook("reflect_y")).prop("checked", this.domain.boundary_condition.reflect_y);
-    $(this.queryByHook("reflect_z")).prop("checked", this.domain.boundary_condition.reflect_z);
-    this.renderDomainTypes();
-    this.renderNewParticle();
-    this.renderEditParticle();
-    this.renderTypeSelectView();
-    this.renderMeshTypeDefaults(0);
-    this.renderMeshTransformations();
-    this.renderTypesFileSelect();
-    this.renderCreate3DDomain();
-    let self = this;
-    if(this.domain.particles.length > 0) {
-      let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
-      app.getXHR(endpoint, {
-        success: function (err, response, body) {
-          self.plot = body.fig;
-          self.displayDomain();
-        }
-      });
-    }else{
-      this.displayDomain();
-    }
-    $(document).ready(function () {
-      $('[data-toggle="tooltip"]').tooltip();
-      $('[data-toggle="tooltip"]').click(function () {
-        $('[data-toggle="tooltip"]').tooltip("hide");
-      });
-    });
-    this.domain.updateValid();
-    this.toggleDomainError();
+    this.renderDomainView();
+    app.documentSetup();
     if(!this.model) {
       $(this.queryByHook("save-to-model")).addClass("disabled")
     }
   },
-  renderTypesFileSelect: function () {
-    let self = this;
-    let endpoint = path.join(app.getApiPath(), "spatial-model/types-list");
-    app.getXHR(endpoint, {
-      success: function (err, response, body) {
-        self.typeDescriptions = body.paths;
-        var typesSelectView = new SelectView({
-          label: '',
-          name: 'type-files',
-          required: false,
-          idAttributes: 'cid',
-          options: body.files,
-          unselectedText: "-- Select Type File --",
-        });
-        app.registerRenderSubview(self, typesSelectView, "types-file-select");
-      }
-    });
-  },
-  renderTypesLocationSelect: function (options) {
-    if(this.typesLocationSelectView) {
-      this.typesLocationSelectView.remove();
-    }
-    this.typesLocationSelectView = new SelectView({
-      label: '',
-      name: 'type-locations',
-      required: false,
-      idAttributes: 'cid',
-      options: options,
-      unselectedText: "-- Select Location --"
-    });
-    app.registerRenderSubview(this, this.typesLocationSelectView, "types-file-location-select")
-  },
-  renderTypeSelectView: function () {
-    if(this.typeView) {
-      this.typeView.remove()
-    }
-    this.typeView = new SelectView({
-      label: 'Type:  ',
-      name: 'type',
-      required: true,
-      idAttribute: 'typeID',
-      textAttribute: 'name',
-      eagerValidate: true,
-      options: this.domain.types,
-      value: this.domain.types.get(0, "typeID")
-    });
-    app.registerRenderSubview(this, this.typeView, "mesh-type-select")
-  },
-  saveDomain: function (name=null) {
+  saveDomain: function ({name=null}={}) {
     let domain = this.domain.toJSON();
     if(name) {
-      let file = name + ".domn";
+      let file = `${name}.domn`;
       var dirname = this.model ? path.dirname(this.model.directory) : this.domain.dirname;
       var domainPath = dirname === "/" ? file : path.join(dirname, file);
     }else{
       var domainPath = this.domain.directory;
     }
-    let self = this;
-    let endpoint = path.join(app.getApiPath(), "file/json-data") + "?path=" + domainPath;
+    let endpoint = path.join(app.getApiPath(), "file/json-data") + `?path=${domainPath}`;
     app.postXHR(endpoint, domain, {
-      success: function (err, response, body) {
-        self.completeAction("Domain save to file (.domn)", "sd");
+      success: (err, response, body) => {
+        this.completeAction("Domain save to file (.domn)");
       },
-      error: function (err, response, body) {
-        self.errorAction(body.Message, "sd");
-        console.log(body.message);
-      }
-    });
-  },
-  selectParticle: function (data) {
-    let point = data.points[0];
-    this.actPart.part = this.domain.particles.get(point.id, "particle_id");
-    this.actPart.tn = point.curveNumber;
-    this.actPart.pn = point.pointNumber;
-    this.renderEditParticle();
-  },
-  setBoundaryCondition: function (e) {
-    let key = e.target.dataset.hook;
-    let value = e.target.checked;
-    this.domain.boundary_condition[key] = value;
-  },
-  setLimitation: function (e) {
-    let data = e.target.parentElement.parentElement.dataset.hook.split('-');
-    let index = data[1] === "min" ? 0 : 1;
-    let value = Number(e.target.value.trim())
-    this.domain[data[0]][index] = value;
-  },
-  setDensity: function (e) {
-    let value = Number(e.target.value)
-    this.domain.rho_0 = value;
-  },
-  setGravity: function (e) {
-    let value = Number(e.target.value)
-    let hook = e.target.parentElement.parentElement.dataset.hook;
-    if(hook.endsWith("x")){
-      this.domain.gravity[0] = value;
-    }else if(hook.endsWith("y")) {
-      this.domain.gravity[1] = value;
-    }else {
-      this.domain.gravity[2] = value;
-    }
-  },
-  setPressure: function (e) {
-    let value = Number(e.target.value)
-    this.domain.p_0 = value;
-  },
-  setSpeed: function (e) {
-    let value = Number(e.target.value)
-    this.domain.c_0 = value;
-  },
-  setStaticDomain: function (e) {
-    let value = e.target.checked;
-    this.domain.statis = value;
-  },
-  startAction: function (action, src) {
-    $(this.queryByHook(src + "-complete")).css("display", "none");
-    $(this.queryByHook(src + "-action-in-progress")).text(action);
-    $(this.queryByHook(src + "-in-progress")).css("display", "inline-block");
-    console.log(action)
-  },
-  unassignAllParticles: function (type, update=true) {
-    let self = this;
-    this.domain.particles.forEach(function (particle) {
-      if(particle.type === type) {
-        self.actPart.part = particle;
-        self.actPart.tn = type;
-        self.actPart.pn = self.plot.data[type].ids.indexOf(particle.particle_id)
-        self.changeParticleType(0);
+      error: (err, response, body) => {
+        this.errorAction(body.Message);
       }
     });
-    if(this.actPart.part && this.actPart.part.type == type) {
-      this.actPart.part = null;
-      this.renderEditParticle();
-    }
-    if(update) {
-      this.updatePlot();
-    }
-  },
-  updatePlot: function () {
-    var el = this.queryByHook("domain-plot");
-    el.removeListener('plotly_click', this.selectParticle);
-    Plotly.purge(el);
-    this.displayDomain();
-  },
-  update: function () {},
-  updateMeshTypeAndDefaults: function (e) {
-    let id = Number(e.target.selectedOptions.item(0).value);
-    this.renderMeshTypeDefaults(id);
-  },
-  updateParticle: function ({cb=null}={}) {
-    if(this.actPart.part.pointChanged) {
-      let x = this.actPart.part.point[0];
-      let y = this.actPart.part.point[1];
-      let z = this.actPart.part.point[2];
-      this.changeParticleLocation(x, y, z)
-    }
-    if(this.actPart.part.typeChanged) {
-      let type = this.actPart.part.type
-      this.changeParticleType(type);
-      this.renderDomainTypes();
-    }
-    this.updatePlot();
-    if(cb) {
-      cb()
-    }
-  },
-  updateValid: function () {},
-  toggleDomainError: function () {
-    let errorMsg = $(this.queryByHook('domain-error'))
-    if(!this.domain.valid) {
-      errorMsg.addClass('component-invalid')
-      errorMsg.removeClass('component-valid')
-    }else{
-      errorMsg.addClass('component-valid')
-      errorMsg.removeClass('component-invalid')
-    }
   },
+  startAction: function (action) {
+    $(this.queryByHook("sd-complete")).css("display", "none");
+    $(this.queryByHook("sd-error")).css("display", "none");
+    $(this.queryByHook("sd-action-in-progress")).text(action);
+    $(this.queryByHook("sd-in-progress")).css("display", "inline-block");
+  }
 });
 
 initPage(DomainEditor);
diff --git a/client/templates/pages/domainEditor.pug b/client/templates/pages/domainEditor.pug
index 8d361c67b0..d97d85b6c2 100644
--- a/client/templates/pages/domainEditor.pug
+++ b/client/templates/pages/domainEditor.pug
@@ -18,287 +18,7 @@ section.page
           li.breadcrumb-item
             a.active-link(data-hook="parent-one-breadcrumb") Parent
 
-  div.card.card-body
-
-    div
-
-      h3.inline Properties
-
-      button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-properties", data-hook="collapse-domain-properties") -
-
-    div.collapse.show(id="domain-properties" data-hook="domain-properties")
-
-      table.table
-        thead
-          tr
-            th(scope="col") Static Domain
-            th(scope="col") Density
-            th(scope="col") Gravity
-            th(scope="col")
-              div
-                div.inline Pressure
-
-                div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.pressure) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
-
-            th(scope="col")
-              div
-                div.inline Speed of Sound
-
-                div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.speed) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
-
-        tbody
-          tr
-            td: input(type="checkbox", id="static-domain", data-hook="static-domain")
-            td: div(data-hook="density")
-            td
-              div(data-target="gravity" data-hook="gravity-x")
-              div(data-target="gravity" data-hook="gravity-y")
-              div(data-target="gravity" data-hook="gravity-z")
-            td: div(data-hook="pressure")
-            td: div(data-hook="speed")
-
-      h4 Domain Limits
-
-      table.table
-        thead
-          tr
-            th(scope="col")
-            th(scope="col") X-Axis
-            th(scope="col") Y-Axis
-            th(scope="col") Z-Axis
-
-        tbody
-          tr
-            th(scope="row") Minimum
-            td: div(data-hook="x_lim-min" data-name="limitation")
-            td: div(data-hook="y_lim-min" data-name="limitation")
-            td: div(data-hook="z_lim-min" data-name="limitation")
-          tr
-            th(scope="row") Maximum
-            td: div(data-hook="x_lim-max" data-name="limitation")
-            td: div(data-hook="y_lim-max" data-name="limitation")
-            td: div(data-hook="z_lim-max" data-name="limitation")
-          tr
-            th(scope="row") Reflect
-            td: input(type="checkbox", id="x-reflect", data-hook="reflect_x" data-target="reflect" disabled)
-            td: input(type="checkbox", id="y-reflect", data-hook="reflect_y" data-target="reflect" disabled)
-            td: input(type="checkbox", id="z-reflect", data-hook="reflect_z" data-target="reflect" disabled)
-
-  div.card.card-body
-
-    div
-
-      h3.inline Types
-
-      button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-types", data-hook="collapse-domain-types") -
-
-    div.collapse.show(id="domain-types" data-hook="domain-types")
-
-      div
-
-        h6(data-hook="unassigned-particles")
-
-        div(data-hook="domain-error"): p.text-danger A domain cannot have any un-assigned particles.
-
-      table.table
-        thead
-          tr
-            th(scope="col") Name
-            th(scope="col") Number of Particles
-            th(scope="col" colspan="4") Defaults
-        
-        tbody(data-hook="domain-types-list")
-
-      button.btn.btn-outline-primary.box-shadow(data-hook="add-domain-type") Add Type
-
-      div.card.card-body(data-hook="edit-defaults" style="display: none")
-
-        h4(data-hook="set-type-defaults-header")
-
-        table.table
-          thead
-            tr
-              th(scope="col") Mass
-              th(scope="col") Volume
-              th(scope="col") Viscosity
-              th(scope="col") Fixed
-
-          tbody
-            tr
-              td: div(data-hook="td-mass")
-              td: div(data-hook="td-vol")
-              td: div(data-hook="td-nu")
-              td: input(type="checkbox" data-hook="td-fixed")
-
-        button.btn.btn-outline-primary.box-shadow(data-hook="set-type-defaults") Submit
-  
-  div.card.card-body
-
-    div
-
-      h3.inline Particles
-
-      button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-particles", data-hook="collapse-domain-particle") -
-
-    div.collapse.show(id="domain-particles" data-hook="domain-particles")
-
-      ul.nav.nav-tabs
-
-        li.nav-item
-
-          a.nav-link.tab.active(data-toggle="tab" href="#new-particle") Create New
-
-        li.nav-item
-
-          a.nav-link.tab(data-toggle="tab" href="#edit-particle") Edit Selected
-
-        li.nav-item
-
-          a.nav-link.tab(data-toggle="tab" href="#set-particle-types") Set Particle Types
-
-        li.nav-item
-
-          a.nav-link.tab(data-toggle="tab" href="#add-3d-domain") Create 3D Domain
-
-        li.nav-item
-
-          a.nav-link.tab(data-toggle="tab" href="#import-particles") Import Mesh
-
-      div.tab-content
-
-        div.tab-pane.active(id="new-particle" data-hook="new-particle")
-
-        div.tab-pane(id="edit-particle" data-hook="edit-particle")
-
-        div.tab-pane(id="add-3d-domain" data-hook="add-3d-domain")
-
-        div.tab-pane(id="set-particle-types" data-hook="set-particle-types")
-
-          div.card.card-body
-
-            div.my-3
-
-              div.text-info(data-hook="type-location-message" style="display: none")
-                | There are multiple type files with that name, please select a location
-
-              div.inline.mr-3
-
-                span.inline.mr-2(for="types-file-select") Select type description file:
-
-                div.inline(id="types-file-select" data-hook="types-file-select")
-
-              div.inline(data-hook="type-location-container" style="display: none")
-
-                span.inlinemr-2(for="types-file-location-select") Location:
-
-                div.inline(id="types-file-location-select" data-hook="types-file-location-select")
-
-            div.inline
-
-              button.btn.btn-outline-primary.box-shadow(data-hook="set-particle-types-btn" disabled) Set Types
-
-            div.mdl-edit-btn.saving-status.inline(data-hook="st-in-progress")
-
-              div.spinner-grow.mr-2
-
-              span(data-hook="st-action-in-progress")
-
-            div.mdl-edit-btn.saved-status.inline(data-hook="st-complete")
-
-              span(data-hook="st-action-complete")
-
-            div.mdl-edit-btn.save-error-status(data-hook="st-error")
-
-              span(data-hook="st-action-error")
-
-        div.tab-pane(id="import-particles")
-
-          div.card.card-body
-
-            div.my-3
-
-              span.inline.mr-2(for="meshfile") Please specify a mesh to import: 
-
-              input(id="meshfile" type="file" name="meshfile" size="30" accept=".xml" required)
-
-            div.mb-3
-
-              span.inline.mr-2(for=typefile) Type descriptions (optional):
-
-              input(id="typefile" type="file" name="typefile" size="30" accept=".txt")
-
-            div
-
-              h4.inline Advanced
-
-              button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#mesh-advanced", data-hook="collapse-mesh-advanced") +
-
-            div.collapse(id="mesh-advanced" data-hook="mesh-advanced-container")
-
-              div(data-hook="mesh-type-select")
-
-              h5 Type Defaults
-
-              table.table
-                thead
-                  tr
-                    th(scope="col") Mass
-                    th(scope="col") Volume
-                    th(scope="col") Viscosity
-                    th(scope="col") Fixed
-
-                tbody
-                  tr
-                    td: div(data-hook="mesh-mass")
-                    td: div(data-hook="mesh-volume")
-                    td: div(data-hook="mesh-nu")
-                    td: input(type="checkbox" data-hook="mesh-fixed" disabled)
-
-              h5 Particle Transformations
-
-              table.table
-                thead
-                  tr
-                    th(scope="col") X-Axis
-                    th(scope="col") Y-Axis
-                    th(scope="col") Z-Axis
-                tbody
-                  tr
-                    td: div(data-hook="mesh-x-trans")
-                    td: div(data-hook="mesh-y-trans")
-                    td: div(data-hook="mesh-z-trans")
-
-            div.inline
-
-              button.btn.btn-outline-primary.box-shadow(data-hook="import-particles-btn" disabled) Import Mesh
-
-            div.mdl-edit-btn.saving-status.inline(data-hook="im-in-progress")
-
-              div.spinner-grow.mr-2
-
-              span(data-hook="im-action-in-progress")
-
-            div.mdl-edit-btn.saved-status.inline(data-hook="im-complete")
-
-              span(data-hook="im-action-complete")
-
-            div.mdl-edit-btn.save-error-status(data-hook="im-error")
-
-              span(data-hook="im-action-error")
-
-  div.card.card-body
-
-    div
-
-      h3.inline Domain
-    
-      button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#domain-plot-container", data-hook="collapse-domain-plot") -
-
-    div.collapse.show(id="domain-plot-container" data-hook="domain-plot-container")
-
-      div(id="domain-plot" data-hook="domain-plot" style="height: 800px")
-
-      div.text-danger(data-hook="domain-plot-empty") The domain currently has no particles to display
+  div(data-hook="domain-view-container")
 
   div.inline
 

From 48272522fcb97afbb3b033a653cceb759ce50192 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 10:07:32 -0400
Subject: [PATCH 045/110] Switched the edit radio input to a checkbox.

---
 client/model-view/templates/editReaction.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/model-view/templates/editReaction.pug b/client/model-view/templates/editReaction.pug
index 0468032826..455489de7d 100644
--- a/client/model-view/templates/editReaction.pug
+++ b/client/model-view/templates/editReaction.pug
@@ -7,7 +7,7 @@ div.mx-1
 
     div.col-sm-1
 
-      div.pl-3: input(type="radio" data-hook="select" data-toggle="collapse" data-target="#collapse-reaction-details" + this.model.compID)
+      div.pl-3: input(type="checkbox" data-hook="select" data-toggle="collapse" data-target="#collapse-reaction-details" + this.model.compID)
 
     div.col-sm-3(data-hook="input-name-container")
 

From ba6a88557d2cdbfc58eff90b067e025abcbce4cd Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 11 Jul 2022 10:37:30 -0400
Subject: [PATCH 046/110] Fixed issue with fixed type default not being set.

---
 client/domain-view/views/type-view.js | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index c5376bb788..0b0656b39d 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -40,6 +40,7 @@ module.exports = View.extend({
   events: {
     'change [data-hook=type-name]' : 'handleRenameType',
     'change [data-target=type-defaults]' : 'updateView',
+    'change [data-hook=td-fixed]' : 'setTDFixed',
     'click [data-hook=select]' : 'selectType',
     'click [data-hook=unassign-all]' : 'handleUnassignParticles',
     'click [data-hook=delete-type]' : 'handleDeleteType',
@@ -57,6 +58,7 @@ module.exports = View.extend({
         setTimeout(_.bind(this.openTypeDetails, this), 1);
       }
     }
+    $(this.queryByHook('view-td-fixed')).prop('checked', this.model.fixed)
     app.documentSetup();
   },
   handleDeleteType: function (e) {
@@ -85,6 +87,10 @@ module.exports = View.extend({
   selectType: function () {
     this.model.selected = !this.model.selected;
   },
+  setTDFixed: function (e) {
+    this.model.fixed = e.target.checked;
+    this.updateView();
+  },
   update: function () {},
   updateValid: function () {},
   updateView: function () {

From 265d15d1c00905273327b25a4ccebf5c77e50733 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Sun, 17 Jul 2022 11:24:16 -0400
Subject: [PATCH 047/110] Updated the SpatialPy version to v1.0.4

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 100e866b42..9ea7f6ee31 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,5 +3,5 @@ python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
 gillespy2==1.6.10
-spatialpy==1.0.3
+spatialpy==1.0.4
 git+https://github.com/StochSS/sciope.git@master

From 108e599e387def15651fef54c571989556c438aa Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 17 Jul 2022 12:18:46 -0400
Subject: [PATCH 048/110] Refactored update domain function to realign domain
 types for front end plotting.  Added domain update call when loading domain
 (.domn) files.

---
 .../handlers/util/stochss_spatial_model.py    | 48 +++++++++++--------
 1 file changed, 27 insertions(+), 21 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index c7de6e5f4a..57f24422d0 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -343,7 +343,9 @@ def __load_domain_from_file(self, path):
             path = os.path.join(self.user_dir, path)
             if path.endswith(".domn"):
                 with open(path, "r", encoding="utf-8") as domain_file:
-                    return json.load(domain_file)
+                    s_domain = json.load(domain_file)
+                    self.__update_domain(domain=s_domain)
+                    return s_domain
             s_domain = Domain.read_xml_mesh(filename=path)
             return self.__build_stochss_domain(s_domain=s_domain)
         except FileNotFoundError as err:
@@ -369,26 +371,30 @@ def __read_model_file(self):
             raise FileNotJSONFormatError(message, traceback.format_exc()) from err
 
 
-    def __update_domain(self):
-        if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6:
-            self.model['domain'] = self.get_model_template()['domain']
-        elif "static" not in self.model['domain'].keys():
-            self.model['domain']['static'] = True
-        if "rho" not in self.model['domain']['types'][0].keys() or \
-                    "c" not in self.model['domain']['types'][0].keys():
-            for d_type in self.model['domain']['types']:
-                if "rho" not in d_type.keys():
-                    d_type['rho'] = d_type['mass'] / d_type['volume']
-                if "c" not in d_type.keys():
-                    d_type['c'] = 10
-        if self.model['domain']['particles']:
-            if "rho" not in self.model['domain']['particles'][0].keys() or \
-                        "c" not in self.model['domain']['particles'][0].keys():
-                for particle in self.model['domain']['particles']:
-                    if "rho" not in particle.keys():
-                        particle['rho'] = particle['mass'] / particle['volume']
-                    if "c" not in particle.keys():
-                        particle['c'] = 10
+    def __update_domain(self, domain=None):
+        if domain is None:
+            if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6:
+                self.model['domain'] = self.get_model_template()['domain']
+            domain = self.model['domain']
+        if "static" not in domain.keys():
+            domain['static'] = True
+        type_changes = {}
+        for i, d_type in enumerate(domain['types']):
+            if d_type['typeID'] != i:
+                type_changes[d_type['typeID']] = i
+                d_type['typeID'] = i
+            if "rho" not in d_type.keys():
+                d_type['rho'] = d_type['mass'] / d_type['volume']
+            if "c" not in d_type.keys():
+                d_type['c'] = 10
+        if domain['particles']:
+            for particle in domain['particles']:
+                if particle['type'] in type_changes:
+                    particle['type'] = type_changes[particle['type']]
+                if "rho" not in particle.keys():
+                    particle['rho'] = particle['mass'] / particle['volume']
+                if "c" not in particle.keys():
+                    particle['c'] = 10
 
 
     def convert_to_model(self):

From c812afc08f496a109272dd59f8fa7173e6676d00 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 17 Jul 2022 12:20:23 -0400
Subject: [PATCH 049/110] Added a function to reailgn types when editing
 domains.

---
 client/models/domain.js | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/client/models/domain.js b/client/models/domain.js
index 738ebbe28d..72ea2428fc 100644
--- a/client/models/domain.js
+++ b/client/models/domain.js
@@ -72,6 +72,23 @@ module.exports = State.extend({
     this.def_type_id += 1;
     return id;
   },
+  realignTypes: function (oldType) {
+    this.def_type_id -= 1;
+    this.types.forEach((type) => {
+      if(type.typeID > oldType) {
+        let id = type.typeID - 1;
+        if(type.name === type.typeID.toString()) {
+          type.name = id.toString();
+        }
+        type.typeID = id;
+      }
+    });
+    this.particles.forEach((particle) => {
+      if(particle.type > oldType) {
+        particle.type -= 1;
+      }
+    });
+  },
   validateModel: function () {
     if(!this.particles.validateCollection()) return false;
     return true;

From 6f1d9a48aa39e78eacab50518059e8f978883005 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 17 Jul 2022 12:21:29 -0400
Subject: [PATCH 050/110] Added realign types function call when types are
 deleted.

---
 client/domain-view/domain-view.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index ee2d3a1767..0897c840f3 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -237,6 +237,7 @@ module.exports = View.extend({
       });
       this.model.particles.removeParticles(particles);
     }
+    this.model.realignTypes(type);
     this.plot.data.splice(type, 1);
     this.renderTypesView();
     this.renderNewParticleView();

From 468c6eafaad3e5c3af05735343e1c1637b5a9b1f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 08:48:42 -0400
Subject: [PATCH 051/110] Added missing else case for handling plots from
 external domains.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index d631a86ecd..93f2d5cb63 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -501,6 +501,8 @@ def get_domain_plot(self, path=None, new=False, domains=None):
             elif path is None:
                 path = self.path
                 s_domain = self.load()['domain']
+            else:
+                s_domain = self.__load_domain_from_file(path)
             try:
                 domain = Domain.read_stochss_domain(path)
             except DomainError as err:

From c4663adce112c00df0c97dd8f620cb43647119c3 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 12:51:19 -0400
Subject: [PATCH 052/110] Refactored the domain viewer in the model view to use
 the new domain view container.

---
 client/model-view/templates/domainViewer.pug |  94 +-----
 client/model-view/views/domain-viewer.js     | 328 +++++++------------
 2 files changed, 120 insertions(+), 302 deletions(-)

diff --git a/client/model-view/templates/domainViewer.pug b/client/model-view/templates/domainViewer.pug
index 41b57b714f..830b30a5b9 100644
--- a/client/model-view/templates/domainViewer.pug
+++ b/client/model-view/templates/domainViewer.pug
@@ -41,101 +41,11 @@ div#domain-viewer.card
 
             div.inline(data-hook="select-location")
 
-      div.row
-
-        div.col-md-4
-
-          h4 Domain Properties
-
-          hr.mt-2
-          div.row
-            div.col-sm-6: h6.pl-2 <b>Static Domain</b>
-            div.col-sm-6: input(type="checkbox" id="static-domain" data-hook="static-domain" checked=this.model.static disabled)
-
-          hr.mt-2
-          div.row
-            div.col-sm-6: h6.pl-2 <b>Density</b>
-            div.col-sm-6=this.model.rho_0
-
-          hr.mt-2
-          div.row
-            div.col-sm-6: h6.pl-2 <b>Gravity</b>
-            div.col-sm-6=this.gravity
-
-          hr.mt-2
-          div.row
-            div.col-sm-6: h6.pl-2 <b>Pressure</b>
-            div.col-sm-6=this.model.p_0
-
-          hr.mt-2
-          div.row
-            div.col-sm-6: h6.pl-2 <b>Speed of Sound</b>
-            div.col-sm-6=this.model.c_0
-
-        div.col-md-8
-
-          h4 Domain Limits
-
-          hr.mt-2
-          div.row.head.mx-1
-            div.col-sm-3
-            div.col-sm-3.pb-1: h6 <b>Minimum</b>
-            div.col-sm-3: h6 <b>Minimum</b>
-            div.col-sm-3: h6 <b>Reflect</b>
-
-          div.row.mt-3
-            div.col-sm-3: h6.pl-2 <b>X-Axis</b>
-            div.col-sm-3=this.model.x_lim[0]
-            div.col-sm-3=this.model.x_lim[1]
-            div.col-sm-3: input(type="checkbox" checked=this.model.boundary_condition.reflect_x disabled)
-
-          hr.mt-2
-          div.row
-            div.col-sm-3: h6.pl-2 <b>Y-Axis</b>
-            div.col-sm-3=this.model.y_lim[0]
-            div.col-sm-3=this.model.y_lim[1]
-            div.col-sm-3: input(type="checkbox" checked=this.model.boundary_condition.reflect_y disabled)
-
-          hr.mt-2
-          div.row
-            div.col-sm-3: h6.pl-2 <b>Z-Axis</b>
-            div.col-sm-3=this.model.z_lim[0]
-            div.col-sm-3=this.model.z_lim[1]
-            div.col-sm-3: input(type="checkbox" checked=this.model.boundary_condition.reflect_z disabled)
-
-      div.mt-3
-
-        h4 Types
-
-        hr
-
-        h6="Number of Un-Assigned Particles: " + this.model.types.get(0, "typeID").numParticles
-
-        div.component-valid(data-hook="domain-error"): p.text-danger A domain cannot have any un-assigned particles.
-
-        hr
-
-        div.mx-1.row.head.align-items-baseline
-
-          div.col-sm-2: h6 <b>Name</b>
-
-          div.col-sm-2: h6 <b>Number of Particles</b>
-
-          div.col-sm-2: h6 <b>Mass</b>
-
-          div.col-sm-2: h6 <b>Volume</b>
-
-          div.col-sm-2: h6 <b>Viscosity</b>
-
-          div.col-sm-2: h6 <b>Fixed</b>
-
-        div.my-3(data-hook="domain-types-list")
+        div(data-hook="domain-view-container")
 
       div.tab-pane.active(id="edit-domain" data-hook="edit-domain")
 
-        hr
-
-        div
+        div.mt-3
 
           button.btn.btn-outline-primary.box-shadow(data-hook="edit-domain-btn") Edit Domain
 
diff --git a/client/model-view/views/domain-viewer.js b/client/model-view/views/domain-viewer.js
index ac4ec74f3d..c2a7d99b18 100644
--- a/client/model-view/views/domain-viewer.js
+++ b/client/model-view/views/domain-viewer.js
@@ -18,48 +18,42 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 let $ = require('jquery');
 let path = require('path');
-let _ = require('underscore');
 //support files
 let app = require('../../app');
-let Plotly = require('../../lib/plotly');
-let Tooltips = require('../../tooltips');
+//models
+let Domain = require('../../models/domain');
 //views
 let View = require('ampersand-view');
 let SelectView = require('ampersand-select-view');
-let TypesViewer = require('../../views/edit-domain-type');
-let ParticleViewer = require('../../views/view-particle');
-let QuickviewDomainTypes = require('../../views/quickview-domain-types');
+let DomainView = require('../../domain-view/domain-view');
 //templates
 let template = require('../templates/domainViewer.pug');
 
 module.exports = View.extend({
   template: template,
   events: {
-    'click [data-hook=domain-edit-tab]' : 'toggleViewExternalDomainBtn',
-    'click [data-hook=domain-view-tab]' : 'toggleViewExternalDomainBtn',
+    'change [data-hook=select-domain]' : 'handleSelectDomain',
+    'change [data-hook=select-location]' : 'handleSelectLocation',
+    'click [data-hook=domain-edit-tab]' : 'handleModeSwitch',
+    'click [data-hook=domain-view-tab]' : 'handleModeSwitch',
     'click [data-hook=collapse]' : 'changeCollapseButtonText',
+    'click [data-hook=select-external-domain]' : 'handleViewExternalDomains',
     'click [data-hook=edit-domain-btn]' : 'editDomain',
     'click [data-hook=create-domain]' : 'editDomain',
-    'click [data-hook=save-to-model]' : 'saveDomainToModel',
-    'click [data-hook=select-external-domain]' : 'handleLoadExternalDomain',
-    'change [data-hook=select-domain]' : 'handleSelectDomain',
-    'change [data-hook=select-location]' : 'handleSelectDomainLocation'
+    'click [data-hook=save-to-model]' : 'saveDomainToModel'
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
     this.readOnly = attrs.readOnly ? attrs.readOnly : false;
-    this.tooltips = Tooltips.domainEditor;
-    this.domainPath = attrs.domainPath;
-    this.plot = Boolean(attrs.domainPlot) ? attrs.domainPlot : null;
-    this.elements = Boolean(attrs.domainElements) ? attrs.domainElements : null;
-    this.model.particles.forEach((particle) => {
-      this.model.types.get(particle.type, "typeID").numParticles += 1;
-    });
-    this.gravity = this.getGravityString();
+    this.elements = attrs.domainElements ? attrs.domainElements : null;
+    this.plot = attrs.domainPlot ? attrs.domainPlot : null;
+    this.domainPath = null;
+    this.domain = null;
+    this.files = null;
+    this.locations = null;
   },
   render: function (attrs, options) {
     View.prototype.render.apply(this, arguments);
-    this.queryStr = `?path=${this.parent.model.directory}`;
     if(this.readOnly) {
       $(this.queryByHook('domain-edit-tab')).addClass("disabled");
       $(".nav .disabled>a").on("click", (e) => {
@@ -69,33 +63,25 @@ module.exports = View.extend({
       $(this.queryByHook('domain-view-tab')).tab('show');
       $(this.queryByHook('edit-domain')).removeClass('active');
       $(this.queryByHook('view-domain')).addClass('active');
-      this.toggleViewExternalDomainBtn();
-    }else {
-      this.renderDomainSelectView();
-      if(this.domainPath) {
-        $(this.queryByHook("domain-container")).collapse("show");
-        $(this.queryByHook("collapse")).text("-");
-        if(this.domainPath !== "viewing") {
-          $(this.queryByHook("save-to-model")).prop("disabled", false);
-          $(this.queryByHook("external-domain-select")).css("display", "block");
-          $(this.queryByHook("select-external-domain")).text("View Model's Domain");
-          this.queryStr += `&domain_path=${this.domainPath}`;
-        }
+      this.toggleViewExternalDomains(this.readOnly);
+    }
+    if(!this.elements) {
+      $(this.queryByHook("view-domain-plot-container")).css('display', 'block');
+      this.elements = {
+        select: $(this.queryByHook("domain-select-particle")),
+        particle: {view: this, hook: "domain-particle-viewer"},
+        figure: this.queryByHook("view-domain-plot"),
+        // figureEmpty: this.queryByHook("domain-plot-container-empty"),
+        type: this.queryByHook("domain-types-quick-view")
       }
-      this.toggleDomainError();
     }
-    this.renderTypesViewer();
-    this.renderPlotParticleViewer();
+    this.renderDomainView();
   },
   changeCollapseButtonText: function (e) {
     app.changeCollapseButtonText(this, e);
   },
-  displayDomain: function (domainPreview) {
-    Plotly.newPlot(domainPreview, this.plot);
-    domainPreview.on('plotly_click', _.bind(this.selectParticle, this));
-  },
   editDomain: function (e) {
-    var queryStr = `?path=${this.parent.model.directory}`;
+    var queryStr = `?path=${this.model.directory}`;
     if(e.target.dataset.hook === "create-domain") {
       queryStr += "&new"
     }else if(this.domainPath) {
@@ -104,45 +90,69 @@ module.exports = View.extend({
     let endpoint = path.join(app.getBasePath(), "stochss/domain/edit") + queryStr;
     window.location.href = endpoint;
   },
-  getDomainSelectValue: function (files) {
-    if(!this.domainPath || this.domainPath === "viewing") {
-      return null;
-    }
-    let domainFile = this.domainPath.split('/').pop();
-    let value = files.filter((file) => {
-      return file[1] === domainFile;
-    })[0][0];
-    return value;
-  },
-  getGravityString: function () {
-    var gravity = `(X: ${this.model.gravity[0]}`;
-    gravity += `, Y: ${this.model.gravity[1]}`;
-    gravity += `, Z: ${this.model.gravity[2]})`;
-    return gravity;
-  },
-  handleLoadExternalDomain: function (e) {
-    let text = e.target.textContent;
-    if(text === "View External Domain") {
-      $(this.queryByHook("external-domain-select")).css("display", "block");
-      $(this.queryByHook("select-external-domain")).text("View Model's Domain");
-    }else{
-      this.reloadDomain("viewing");
+  handleModeSwitch: function (e) {
+    if(!e.target.classList.contains('active')) {
+      this.toggleViewExternalDomains(e.target.text === "View");
     }
   },
   handleSelectDomain: function (e) {
     let value = e.srcElement.value;
     if(value) {
-      if(this.externalDomains[value].length <= 1) {
-        this.reloadDomain(this.externalDomains[value][0]);
+      if(this.locations[value].length <= 1) {
+        $(this.queryByHook('select-location-message')).css('display', 'none');
+        $(this.queryByHook('select-domain-location')).css('display', 'none');
+        this.domainPath = this.locations[value][0];
+        this.loadExternalDomainModel();
+      }else{
+        this.renderDomainLocationSelectView(this.locations[value]);
+      }
+    }
+  },
+  handleSelectLocation: function (e) {
+    this.domainPath = e.srcElement.value;
+    this.loadExternalDomainModel();
+  },
+  handleViewExternalDomains: function (e) {
+    let display = e.target.textContent === "View External Domain";
+    if(display) {
+      $(this.queryByHook('select-external-domain')).text("View Model's Domain");
+      if(!this.files) {
+        this.loadExternalDomainFiles();
       }else{
-        $(this.queryByHook("select-location-message")).css('display', "block");
-        $(this.queryByHook("select-domain-location")).css("display", "inline-block");
-        this.renderDomainLocationSelectView(this.externalDomains[value]);
+        this.renderDomainFileSelectView();
       }
+    }else{
+      $(this.queryByHook('select-external-domain')).text("View External Domain");
+      this.domain = null;
+      this.domainPath = null;
+      $(this.queryByHook('select-location-message')).css('display', 'none');
+      $(this.queryByHook('select-domain-location')).css('display', 'none');
+      $(this.queryByHook('external-domain-select')).css('display', 'none');
+      $(this.queryByHook('save-to-model')).prop('disabled', true);
+      this.renderDomainView();
     }
   },
-  handleSelectDomainLocation: function (e) {
-    this.reloadDomain(e.srcElement.value);
+  loadExternalDomainFiles: function () {
+    let endpoint = path.join(app.getApiPath(), "spatial-model/domain-list");
+    app.getXHR(endpoint, {
+      always: (err, response, body) => {
+        this.files = body.files;
+        this.locations = body.paths;
+        this.renderDomainFileSelectView();
+      }
+    });
+  },
+  loadExternalDomainModel: function () {
+    let queryStr = `?path=${this.model.directory}&domain_path=${this.domainPath}`;
+    let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + queryStr;
+    app.getXHR(endpoint, {
+      always: (err, response, body) => {
+        console.log(body)
+        this.domain = new Domain(body.domain);
+        this.renderDomainView({modelsDomain: false});
+        $(this.queryByHook('save-to-model')).prop('disabled', false);
+      }
+    });
   },
   openSection: function () {
     if(!$(this.queryByHook("domain-container")).hasClass("show")) {
@@ -152,162 +162,60 @@ module.exports = View.extend({
     }
     app.switchToEditTab(this, "domain");
   },
-  reloadDomain: function (domainPath) {
-    if(this.domainPath !== domainPath || domainPath === "viewing") {
-      if(this.plot) {
-        let el = this.elements === null ? this.queryByHook("view-domain-plot") : this.elements.plot;
-        el.removeListener('plotly_click', this.selectParticle);
-        Plotly.purge(el);
-        this.plot = null;
-        this.model.types.forEach(function (type) {
-          type.numParticles = 0;
-        });
-      }
-      this.parent.renderDomainViewer(domainPath);
+  renderDomainFileSelectView: function () {
+    if(this.domainFileSelectView) {
+      this.domainFileSelectView.remove();
     }
+    this.domainFileSelectView = new SelectView({
+      name: 'domain-files',
+      required: false,
+      idAttributes: 'cid',
+      options: this.files,
+      unselectedText: '-- Select Domain --'
+    });
+    app.registerRenderSubview(this, this.domainFileSelectView, 'select-domain');
+    $(this.queryByHook('external-domain-select')).css('display', 'block');
   },
   renderDomainLocationSelectView: function (options) {
     if(this.domainLocationSelectView) {
       this.domainLocationSelectView.remove();
     }
     this.domainLocationSelectView = new SelectView({
-      name: 'locations',
+      name: 'file-locations',
       required: false,
       idAttributes: 'cid',
       options: options,
       unselectedText: "-- Select Location --"
     });
     app.registerRenderSubview(this, this.domainLocationSelectView, "select-location");
-  },
-  renderDomainSelectView: function () {
-    let endpoint = path.join(app.getApiPath(), "spatial-model/domain-list");
-    app.getXHR(endpoint, {
-      always: (err, response, body) => {
-        this.externalDomains = body.paths;
-        let domainSelectView = new SelectView({
-          name: 'domains',
-          required: false,
-          idAttributes: 'cid',
-          options: body.files,
-          unselectedText: "-- Select Domain --",
-          value: this.getDomainSelectValue(body.files)
-        });
-        app.registerRenderSubview(this, domainSelectView, "select-domain");
-      }
+    $(this.queryByHook('select-location-message')).css('display', 'block');
+    $(this.queryByHook('select-domain-location')).css('display', 'inline-block');
+  },
+  renderDomainView: function ({modelsDomain=true}={}) {
+    if(this.domainView) {
+      this.domainView.remove();
+    }
+    let domain = modelsDomain ? this.model.domain : this.domain;
+    var queryStr = `?path=${this.model.directory}`;
+    if(!modelsDomain) {
+      queryStr += `&domain_path=${this.domainPath}`;
+    }
+    this.domainView = new DomainView({
+      model: domain,
+      readOnly: true,
+      elements: this.elements,
+      plot: this.plot,
+      queryStr: queryStr
     });
-  },
-  renderLocalParticlesViewer: function ({particle=null}) {
-    if(particle){
-      $(this.queryByHook("domain-select-particle")).css("display", "none");
-      this.particleViewer = new ParticleViewer({
-        model: particle
-      });
-      app.registerRenderSubview(this, this.particleViewer, "domain-particle-viewer");
-    }else{
-      $(this.queryByHook("domain-select-particle")).css("display", "block");
-      this.typeQuickViewer = this.renderCollection(
-        this.model.types,
-        QuickviewDomainTypes,
-        this.queryByHook("domain-types-quick-view")
-      );
-    }
-  },
-  renderMEParticlesViewer: function ({particle=null}) {
-    if(particle){
-      this.elements.select.css("display", "none");
-      this.particleViewer = new ParticleViewer({
-        model: particle
-      });
-      app.registerRenderSubview(this.elements.particle.view, this.particleViewer, this.elements.particle.hook);
-    }else{
-      this.elements.select.css("display", "block");
-      this.typeQuickViewer = this.renderCollection(
-        this.model.types,
-        QuickviewDomainTypes,
-        this.elements.type
-      );
-    }
-  },
-  renderPlot: function (plotElement) {
-    if(this.model.particles.length <= 0) {
-      return
-    }
-    $(this.parent.domainElements.plotEmpty).css('display', 'none');
-    if(this.plot === null) {
-      let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
-      app.getXHR(endpoint, {
-        always: (err, response, body) => {
-          this.plot = body.fig;
-          this.displayDomain(plotElement);
-        }
-      });
-    }else{
-      this.displayDomain(plotElement);
-    }
-  },
-  renderPlotParticleViewer: function ({particle=null}={}) {
-    if(this.particleViewer) {
-      this.particleViewer.remove();
-    }
-    if(this.typeQuickViewer) {
-      this.typeQuickViewer.remove();
-    }
-    if(this.elements === null) {
-      $(this.queryByHook("view-domain-plot-container")).css('display', 'block');
-      this.renderLocalParticlesViewer({particle: particle});
-      if(particle === null) {
-        this.renderPlot(this.queryByHook("view-domain-plot"));
-      }
-    }else{
-      this.renderMEParticlesViewer({particle: particle});
-      if(particle === null) {
-        this.renderPlot(this.elements.plot);
-      }
-    }
-  },
-  renderTypesViewer: function () {
-    if(this.typesViewer) {
-      this.typesViewer.remove();
-    }
-    this.typesViewer = this.renderCollection(
-      this.model.types,
-      TypesViewer,
-      this.queryByHook("domain-types-list"),
-      {filter: (model) => {
-        return model.typeID != 0;
-      }, viewOptions: {viewMode: true}}
-    );
+    app.registerRenderSubview(this, this.domainView, "domain-view-container");
   },
   saveDomainToModel: function (e) {
-    this.parent.model.domain = this.model;
+    this.model.domain = this.domain;
     this.parent.parent.clickSaveHandler(e);
-    this.reloadDomain();
+    this.renderDomainView();
   },
-  selectParticle: function (data) {
-    let point = data.points[0];
-    let particle = this.model.particles.get(point.id, "particle_id");
-    this.renderPlotParticleViewer({particle: particle});
-  },
-  toggleDomainError: function () {
-    let errorMsg = $(this.queryByHook('domain-error'));
-    this.model.updateValid();
-    if(!this.model.valid) {
-      errorMsg.addClass('component-invalid');
-      errorMsg.removeClass('component-valid');
-    }else{
-      errorMsg.addClass('component-valid');
-      errorMsg.removeClass('component-invalid');
-    }
+  toggleViewExternalDomains: function (hide) {
+    let display = hide ? "none" : "block";
+    $(this.queryByHook('external-domains-container')).css('display', display);
   },
-  toggleViewExternalDomainBtn: function (e) {
-    if(e) {
-      if(!e.target.classList.contains("active")) {
-        let display = e.target.text === "View" ? "none" : "block";
-        $(this.queryByHook("external-domains-container")).css("display", display);
-      }
-    }else{
-      let display = this.readOnly ? "none" : "block";
-      $(this.queryByHook("external-domains-container")).css("display", display);
-    }
-  }
 });
\ No newline at end of file

From bc5e3ccd4589513c6f045c61a38af2c8b70e417e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 12:55:26 -0400
Subject: [PATCH 053/110] Refactored the render domain viewer function to work
 with the new domain viewer and domain view.

---
 client/model-view/model-view.js | 36 ++++++++-------------------------
 1 file changed, 8 insertions(+), 28 deletions(-)

diff --git a/client/model-view/model-view.js b/client/model-view/model-view.js
index ee749e91a9..4f393386ce 100644
--- a/client/model-view/model-view.js
+++ b/client/model-view/model-view.js
@@ -170,34 +170,14 @@ module.exports = View.extend({
     if(this.domainViewer) {
       this.domainViewer.remove();
     }
-    if(domainPath && domainPath !== "viewing") {
-      let queryStr = `?path=${this.model.directory}&domain_path=${domainPath}`;
-      let endpoint = path.join(app.getApiPath(), "spatial-model/load-domain") + queryStr;
-      app.getXHR(endpoint, {
-        always: (err, response, body) => {
-          let domain = new Domain(body.domain);
-          this.domainViewer = new DomainViewer({
-            parent: this,
-            model: domain,
-            domainPath: domainPath,
-            readOnly: this.readOnly,
-            domainElements: this.domainElements,
-            domainPlot: this.domainPlot
-          });
-          app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container');
-        }
-      });
-    }else{
-      this.domainViewer = new DomainViewer({
-        parent: this,
-        model: this.model.domain,
-        domainPath: domainPath,
-        readOnly: this.readOnly,
-        domainElements: this.domainElements,
-        domainPlot: this.domainPlot
-      });
-      app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container');
-    }
+    this.domainViewer = new DomainViewer({
+      parent: this,
+      model: this.model,
+      readOnly: this.readOnly,
+      domainElements: this.domainElements,
+      domainPlot: this.domainPlot
+    });
+    app.registerRenderSubview(this, this.domainViewer, 'domain-viewer-container');
   },
   renderEventsView: function () {
     if(this.model.is_spatial) { return };

From 7459d2fb5608311e9536e77d24686aebbd29559c Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 13:09:11 -0400
Subject: [PATCH 054/110] Replaced the types table with a div contained for
 types quickview.

---
 client/templates/pages/modelEditor.pug | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/client/templates/pages/modelEditor.pug b/client/templates/pages/modelEditor.pug
index 2031b051b8..306bb6e24b 100644
--- a/client/templates/pages/modelEditor.pug
+++ b/client/templates/pages/modelEditor.pug
@@ -52,8 +52,7 @@ section.page
 
               h4 Particles per Type
 
-              table.table
-                tbody(data-hook="me-types-quick-view")
+              div(data-hook="me-types-quick-view")
 
     div(data-hook="model-run-container")
 

From f8c6a04d9729310f32cce11a178dbfcfae276106 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 13:12:14 -0400
Subject: [PATCH 055/110] Refacted the domain elements to comply with the new
 domain view.

---
 client/pages/model-editor.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/pages/model-editor.js b/client/pages/model-editor.js
index f473f368a1..63e41c697b 100644
--- a/client/pages/model-editor.js
+++ b/client/pages/model-editor.js
@@ -330,8 +330,8 @@ let ModelEditor = PageView.extend({
     let domainElements = {
       select: $(this.queryByHook("me-select-particle")),
       particle: {view: this, hook: "me-particle-viewer"},
-      plot: this.queryByHook("domain-plot-container"),
-      plotEmpty: this.queryByHook("domain-plot-container-empty"),
+      figure: this.queryByHook("domain-plot-container"),
+      figureEmpty: this.queryByHook("domain-plot-container-empty"),
       type: this.queryByHook("me-types-quick-view")
     }
     this.modelView = new ModelView({

From a61f144cc19928fc0930114c75a1b437b1b95362 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 13:17:44 -0400
Subject: [PATCH 056/110] Refocted the types quickview files to include the new
 particle properties and moved the files to the domain view directory.

---
 client/domain-view/templates/quickviewType.pug           | 9 +++++++++
 .../views/quickview-type.js}                             | 4 ++--
 client/templates/includes/quickviewDomainTypes.pug       | 5 -----
 3 files changed, 11 insertions(+), 7 deletions(-)
 create mode 100644 client/domain-view/templates/quickviewType.pug
 rename client/{views/quickview-domain-types.js => domain-view/views/quickview-type.js} (87%)
 delete mode 100644 client/templates/includes/quickviewDomainTypes.pug

diff --git a/client/domain-view/templates/quickviewType.pug b/client/domain-view/templates/quickviewType.pug
new file mode 100644
index 0000000000..391b93bbc7
--- /dev/null
+++ b/client/domain-view/templates/quickviewType.pug
@@ -0,0 +1,9 @@
+div
+
+  hr
+
+  div.row.mx-1
+
+    div.col-sm-6=this.model.name
+
+    div.col-sm-6=this.model.numParticles
diff --git a/client/views/quickview-domain-types.js b/client/domain-view/views/quickview-type.js
similarity index 87%
rename from client/views/quickview-domain-types.js
rename to client/domain-view/views/quickview-type.js
index ee7f17446f..1e0f17bc6c 100644
--- a/client/views/quickview-domain-types.js
+++ b/client/domain-view/views/quickview-type.js
@@ -17,9 +17,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
 //views
-var View = require('ampersand-view');
+let View = require('ampersand-view');
 //templates
-var template = require('../templates/includes/quickviewDomainTypes.pug');
+let template = require('../templates/quickviewType.pug');
 
 module.exports = View.extend({
   template: template,
diff --git a/client/templates/includes/quickviewDomainTypes.pug b/client/templates/includes/quickviewDomainTypes.pug
deleted file mode 100644
index 80ad38e1f0..0000000000
--- a/client/templates/includes/quickviewDomainTypes.pug
+++ /dev/null
@@ -1,5 +0,0 @@
-tr
-  
-  td=this.model.name
-
-  td=this.model.numParticles
\ No newline at end of file

From f34fa8389868be4f2f46018c3f4d8b31ee001d80 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 13:23:41 -0400
Subject: [PATCH 057/110] Refacted the view particle files to include the new
 particle properties and moved the files to the domain view directory.

---
 client/domain-view/templates/viewParticle.pug | 117 ++++++++++++++++++
 .../{ => domain-view}/views/view-particle.js  |   4 +-
 client/templates/includes/viewParticle.pug    |  30 -----
 3 files changed, 119 insertions(+), 32 deletions(-)
 create mode 100644 client/domain-view/templates/viewParticle.pug
 rename client/{ => domain-view}/views/view-particle.js (89%)
 delete mode 100644 client/templates/includes/viewParticle.pug

diff --git a/client/domain-view/templates/viewParticle.pug b/client/domain-view/templates/viewParticle.pug
new file mode 100644
index 0000000000..fd290ef052
--- /dev/null
+++ b/client/domain-view/templates/viewParticle.pug
@@ -0,0 +1,117 @@
+div
+
+  h5 Properties
+
+  hr.mt-2.mb-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 ID:
+
+    div.col-sm-6
+
+      div.inline=this.model.particle_id
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Type:
+
+    div.col-sm-6
+
+      div.inline=this.type
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Location:
+
+    div.col-sm-6
+
+      div.inline
+
+        div=`X: ${this.model.point[0]}`
+
+        div=`Y: ${this.model.point[1]}`
+
+        div=`Z: ${this.model.point[2]}`
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Mass:
+
+    div.col-sm-6
+
+      div.inline=this.model.mass
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Volume:
+
+    div.col-sm-6
+
+      div.inline=this.model.volume
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Density:
+
+    div.col-sm-6
+
+      div.inline=this.model.rho
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Viscosity:
+
+    div.col-sm-6
+
+      div.inline=this.model.nu
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Speed of Sound:
+
+    div.col-sm-6
+
+      div.inline=this.model.c
+
+  hr.my-1
+
+  div.row.mx-1
+
+    div.col-sm-6
+
+      h6 Fixed:
+
+    div.col-sm-6
+
+      input.inline(type="checkbox" checked=this.model.fixed disabled)
diff --git a/client/views/view-particle.js b/client/domain-view/views/view-particle.js
similarity index 89%
rename from client/views/view-particle.js
rename to client/domain-view/views/view-particle.js
index d832472fda..68cd5c7d7a 100644
--- a/client/views/view-particle.js
+++ b/client/domain-view/views/view-particle.js
@@ -17,9 +17,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
 //views
-var View = require('ampersand-view');
+let View = require('ampersand-view');
 //templates
-var template = require('../templates/includes/viewParticle.pug');
+let template = require('../templates/viewParticle.pug');
 
 module.exports = View.extend({
   template: template,
diff --git a/client/templates/includes/viewParticle.pug b/client/templates/includes/viewParticle.pug
deleted file mode 100644
index 7049a0fb5d..0000000000
--- a/client/templates/includes/viewParticle.pug
+++ /dev/null
@@ -1,30 +0,0 @@
-div
-
-  h5 Properties
-
-  table.table
-    tbody
-      tr
-        th(scope="row") ID
-        td=this.model.particle_id
-      tr
-        th(scope="row") Type
-        td=this.type
-      tr
-        th(scope="row") Location
-        td
-          div="x: " + this.model.point[0]
-          div="y: " + this.model.point[1]
-          div="z: " + this.model.point[2]
-      tr
-        th(scope="row") Mass
-        td=this.model.mass
-      tr
-        th(scope="row") Volume
-        td=this.model.volume
-      tr
-        th(scope="row") Viscosity
-        td=this.model.nu
-      tr
-        th(scope="row") Fixed
-        td: input(type="checkbox" checked=this.model.fixed disabled)
\ No newline at end of file

From 04f6aeed2bf4a10885228e7333e0c95b9e880034 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 18 Jul 2022 13:26:34 -0400
Subject: [PATCH 058/110] Added function to properly render the types quickview
 and view particles sections.  Added functions to hide the particle and domain
 section when in read only mode.

---
 client/domain-view/domain-view.js | 48 +++++++++++++++++++++++++++----
 client/domain-view/domainView.pug |  4 +--
 2 files changed, 44 insertions(+), 8 deletions(-)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index 0897c840f3..9c8a1c8d67 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -28,8 +28,10 @@ let Particle = require('../models/particle');
 let View = require('ampersand-view');
 let TypesView = require('./views/types-view');
 let LimitsView = require('./views/limits-view');
+let QuickviewType = require('./views/quickview-type');
 let PropertiesView = require('./views/properties-view');
 let EditParticleView = require('./views/particle-view');
+let ViewParticleView = require('./views/view-particle');
 let ImportMeshView = require('./views/import-mesh-view');
 let Edit3DDomainView = require('./views/edit-3D-domain-view');
 let TypesDescriptionView = require('./views/types-description-view');
@@ -48,6 +50,7 @@ module.exports = View.extend({
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
     this.readOnly = attrs.readOnly ? attrs.readOnly : false;
+    this.plot = attrs.plot ? attrs.plot : null;
     this.elements = attrs.elements ? attrs.elements : null;
     this.queryStr = attrs.queryStr;
     this.newPart = this.createNewParticle();
@@ -59,7 +62,11 @@ module.exports = View.extend({
     this.renderPropertiesView();
     this.renderLimitsView();
     this.renderTypesView();
-    if(!this.readOnly) {
+    if(this.readOnly) {
+      $(this.queryByHook('domain-particles-editor')).css('display', 'none');
+      $(this.queryByHook('domain-figure-preview')).css('display', 'none');
+      this.renderTypesQuickview();
+    }else{
       this.renderNewParticleView();
       this.renderEditParticleView();
       this.renderTypesDescriptionView();
@@ -73,11 +80,15 @@ module.exports = View.extend({
       }
     }
     let endpoint = path.join(app.getApiPath(), "spatial-model/domain-plot") + this.queryStr;
-    app.getXHR(endpoint, {success: (err, response, body) => {
-      this.plot = body.fig;
-      this.traceTemp = body.trace_temp;
+    if(this.plot) {
       this.displayFigure();
-    }});
+    }else{
+      app.getXHR(endpoint, {success: (err, response, body) => {
+        this.plot = body.fig;
+        this.traceTemp = body.trace_temp;
+        this.displayFigure();
+      }});
+    }
   },
   add3DDomain: function (limits, particles) {
     let limitsChanged = this.changeDomainLimits(limits, Boolean(plot));
@@ -372,6 +383,17 @@ module.exports = View.extend({
     this.typesDescriptionView = new TypesDescriptionView();
     app.registerRenderSubview(this, this.typesDescriptionView, "particle-types-container");
   },
+  renderTypesQuickview: function () {
+    if(this.typesQuickviewView) {
+      this.typesQuickviewView.remove();
+    } 
+    this.elements.select.css('display', 'block');
+    this.typesQuickviewView = this.renderCollection(
+      this.model.types,
+      QuickviewType,
+      this.elements.type
+    );
+  },
   renderTypesView: function () {
     if(this.typesView) {
       this.typesView.remove();
@@ -397,6 +419,16 @@ module.exports = View.extend({
     });
     app.registerRenderSubview(this, this.typesView, "domain-types-container");
   },
+  renderViewParticleView: function () {
+    if(this.viewParticleView) {
+      this.viewParticleView.remove();
+    }
+    this.elements.select.css('display', 'none');
+    this.viewParticleView = new ViewParticleView({
+      model: this.actPart.part
+    });
+    app.registerRenderSubview(this.elements.particle.view, this.viewParticleView, this.elements.particle.hook);
+  },
   resetFigure: function () {
     this.removeFigure();
     this.displayFigure();
@@ -406,7 +438,11 @@ module.exports = View.extend({
     this.actPart.part = this.model.particles.get(point.id, 'particle_id');
     this.actPart.tn = point.curveNumber;
     this.actPart.pn = point.pointNumber;
-    this.renderEditParticleView();
+    if(this.readOnly) {
+      this.renderViewParticleView();
+    }else{
+      this.renderEditParticleView();
+    }
   },
   setParticleTypes: function (typeIDs, types) {
     this.addMissingTypes(typeIDs);
diff --git a/client/domain-view/domainView.pug b/client/domain-view/domainView.pug
index 6ca9c7a9ab..cf03c36301 100644
--- a/client/domain-view/domainView.pug
+++ b/client/domain-view/domainView.pug
@@ -6,7 +6,7 @@ div#domain-view
 
   div(data-hook="domain-types-container")
 
-  div#domain-particles-editor.card
+  div#domain-particles-editor.card(data-hook="domain-particles-editor")
 
     div.card-header.pb-0
 
@@ -101,7 +101,7 @@ div#domain-view
 
           div(data-hook="import-particles-container")
 
-  div#domain-figure-preview.card
+  div#domain-figure-preview.card(data-hook="domain-figure-preview")
 
     div.card-header.pb-0
 

From d0ec835bb1b122ba6229f5d9fadebb376779e5b1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:19:36 -0400
Subject: [PATCH 059/110] Added a handle function to handle apply geometry
 click events.

---
 client/domain-view/views/type-view.js | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 0b0656b39d..8754919217 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -48,12 +48,12 @@ module.exports = View.extend({
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
-    this.vieWMode = attrs.viewMode ? attrs.viewMode : false;
+    this.viewMode = attrs.viewMode ? attrs.viewMode : false;
   },
   render: function (attrs, options) {
-    this.template = this.vieWMode ? viewTemplate : editTemplate;
+    this.template = this.viewMode ? viewTemplate : editTemplate;
     View.prototype.render.apply(this, arguments);
-    if(!this.vieWMode) {
+    if(!this.viewMode) {
       if(this.model.selected) {
         setTimeout(_.bind(this.openTypeDetails, this), 1);
       }
@@ -61,6 +61,19 @@ module.exports = View.extend({
     $(this.queryByHook('view-td-fixed')).prop('checked', this.model.fixed)
     app.documentSetup();
   },
+  handleAddGeometry: function (e) {
+    let particles = this.model.collection.parent.particles.toJSON();
+    let data = {particles: particles, type: this.model.toJSON()}
+    let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
+    app.postXHR(endpoint, data, {
+      success: (err, response, body) => {
+        console.log(body);
+      },
+      error: (err, response, body) => {
+        console.log(body);
+      }
+    });
+  },
   handleDeleteType: function (e) {
     let type = Number(e.target.dataset.type);
     this.model.collection.removeType(this.model);

From 0782cc23244209b34defe838d9b87efec736d27a Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:23:52 -0400
Subject: [PATCH 060/110] Added api handler and route for applying geometries.

---
 stochss/handlers/__init__.py |  1 +
 stochss/handlers/models.py   | 27 +++++++++++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py
index 7804672c54..2d1ac08be9 100644
--- a/stochss/handlers/__init__.py
+++ b/stochss/handlers/__init__.py
@@ -86,6 +86,7 @@ def get_page_handlers(route_start):
         (r"/stochss/api/spatial-model/particle-types\/?", GetParticlesTypesAPIHandler),
         (r"/stochss/api/spatial-model/import-mesh\/?", ImportMeshAPIHandler),
         (r"/stochss/api/spatial-model/3d-domain\/?", Create3DDomainAPIHandler),
+        (r"/stochss/api/spatial-model/apply-geometry\/?", ApplyGeometryAPIHandler),
         (r"/stochss/api/project/new-project\/?", NewProjectAPIHandler),
         (r"/stochss/api/project/load-project\/?", LoadProjectAPIHandler),
         (r"/stochss/api/project/load-browser\/?", LoadProjectBrowserAPIHandler),
diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 4072f163af..7105e23df7 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -483,3 +483,30 @@ async def post(self):
         except StochSSAPIError as err:
             report_error(self, log, err)
         self.finish()
+
+class ApplyGeometryAPIHandler(APIHandler):
+    '''
+    ################################################################################################
+    Handler apply type and properties to particles.
+    ################################################################################################
+    '''
+    @web.authenticated
+    async def post(self):
+        '''
+        Apply type and properties to particles.
+
+        Attributes
+        ----------
+        '''
+        self.set_header('Content-Type', 'application/json')
+        data = json.loads(self.request.body.decode())
+        log.debug(f"Type used to apply geometry: {data['type']}")
+        try:
+            log.info("Applying type and properties to particles.")
+            resp = StochSSSpatialModel.apply_geometry(data['particles'], data['type'])
+            log.info("Successfully applied type and properties to particles.")
+            log.debug(f"Response Message: {resp}")
+            self.write(resp)
+        except StochSSAPIError as err:
+            report_error(self, log, err)
+        self.finish()

From ab05b2696cf7c3b3f05ccf9d540deb9f901e4a78 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:26:44 -0400
Subject: [PATCH 061/110] Added function to apply geometries to particles.

---
 stochss/handlers/util/stochss_spatial_model.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 93f2d5cb63..bd1bfbe807 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -400,6 +400,22 @@ def __update_domain(self, domain=None):
                     particle['c'] = 10
 
 
+    @classmethod
+    def apply_geometry(cls, particles, d_type):
+        def inside(point):
+            namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
+            return eval(d_type['geometry'], locals=namespace)
+        for particle in particles:
+            if inside(particle['point']):
+                particle['type'] = d_type['typeID']
+                particle['mass'] = d_type['mass']
+                particle['volume'] = d_type['volume']
+                particle['rho'] = d_type['rho']
+                particle['nu'] = d_type['nu']
+                particle['c'] = d_type['c']
+                particle['fixed'] = d_type['fixed']
+        return {'particles': particles}
+
     def convert_to_model(self):
         '''
         Convert a spatial model to a non_spatial model

From 96e25b479ff25f352a1ddf55e37c002fc9e92017 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:44:29 -0400
Subject: [PATCH 062/110] Added model support for geometry in types.

---
 client/models/domain-type.js  | 1 +
 client/models/domain-types.js | 1 +
 2 files changed, 2 insertions(+)

diff --git a/client/models/domain-type.js b/client/models/domain-type.js
index 2d9536d0be..16584666e4 100644
--- a/client/models/domain-type.js
+++ b/client/models/domain-type.js
@@ -23,6 +23,7 @@ module.exports = State.extend({
   props: {
     c: 'number',
     fixed: 'boolean',
+    geometry: 'string',
     mass: 'number',
     name: 'string',
     nu: 'number',
diff --git a/client/models/domain-types.js b/client/models/domain-types.js
index df5cf24b13..9ec4e5ac59 100644
--- a/client/models/domain-types.js
+++ b/client/models/domain-types.js
@@ -30,6 +30,7 @@ module.exports = Collection.extend({
     let type = new Type({
         c: 10,
         fixed: false,
+        geometry: "",
         mass: 1.0,
         name: name,
         nu: 0.0,

From feb876df4883e94a0596cacd0b82c093b94fcd75 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:49:57 -0400
Subject: [PATCH 063/110] Added backward compatability for geometries in types.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index bd1bfbe807..50d7777a40 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -390,6 +390,8 @@ def __update_domain(self, domain=None):
                 d_type['rho'] = d_type['mass'] / d_type['volume']
             if "c" not in d_type.keys():
                 d_type['c'] = 10
+            if "geometry" not in d_type.keys():
+                d_type['geometry'] = ""
         if domain['particles']:
             for particle in domain['particles']:
                 if particle['type'] in type_changes:

From 48d97603240ff2b5505ed3972e44558da7adf8fe Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 10:53:01 -0400
Subject: [PATCH 064/110] Added UI support for geometry and the apply geometry
 button.

---
 client/domain-view/templates/editType.pug | 16 +++++++++++++++-
 client/domain-view/views/type-view.js     | 17 ++++++++++++++++-
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 5316ee01e5..9c2232ced2 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -93,4 +93,18 @@ div.mx-1
 
         div.col-sm-2
 
-          input(type="checkbox" data-hook="td-fixed")
\ No newline at end of file
+          input(type="checkbox" data-hook="td-fixed")
+
+      hr
+
+      div.row.align-items-baseline
+
+        div.col-sm-10.align-items-baseline
+
+          h6.inline.mr-3 <b>Geometry</b>:
+
+          div.inline(id="type-geometry" data-hook="type-geometry")
+
+        div.col-sm-2
+
+          button.btn.btn-outline-secondary.box-shadow(data-hook="apply-geometry") Apply
diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 8754919217..0120c1ecc4 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -17,6 +17,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
 let $ = require('jquery');
+let path = require('path');
 let _ = require('underscore');
 //support files
 let app = require('../../app');
@@ -45,6 +46,7 @@ module.exports = View.extend({
     'click [data-hook=unassign-all]' : 'handleUnassignParticles',
     'click [data-hook=delete-type]' : 'handleDeleteType',
     'click [data-hook=delete-all]' : 'handleDeleteTypeAndParticle',
+    'click [data-hook=apply-geometry]' : 'handleApplyGeometry'
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
@@ -61,7 +63,7 @@ module.exports = View.extend({
     $(this.queryByHook('view-td-fixed')).prop('checked', this.model.fixed)
     app.documentSetup();
   },
-  handleAddGeometry: function (e) {
+  handleApplyGeometry: function (e) {
     let particles = this.model.collection.parent.particles.toJSON();
     let data = {particles: particles, type: this.model.toJSON()}
     let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
@@ -192,6 +194,19 @@ module.exports = View.extend({
           value: this.model.c
         });
       }
+    },
+    inputGeometry: {
+      hook: 'type-geometry',
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: false,
+          name: 'geometry',
+          modelKey: 'geometry',
+          valueType: 'string',
+          value: this.model.geometry
+        });
+      }
     }
   }
 });
\ No newline at end of file

From b1cfeabf9def3607cdebb5ef9aaf41714dd72b99 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 13:27:12 -0400
Subject: [PATCH 065/110] Simplified the backend apply geometry function to
 only return a list of changed ids.

---
 stochss/handlers/util/stochss_spatial_model.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 50d7777a40..c9f14b6dae 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -406,17 +406,12 @@ def __update_domain(self, domain=None):
     def apply_geometry(cls, particles, d_type):
         def inside(point):
             namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
-            return eval(d_type['geometry'], locals=namespace)
+            return eval(d_type['geometry'], {}, namespace)
+        ids = []
         for particle in particles:
             if inside(particle['point']):
-                particle['type'] = d_type['typeID']
-                particle['mass'] = d_type['mass']
-                particle['volume'] = d_type['volume']
-                particle['rho'] = d_type['rho']
-                particle['nu'] = d_type['nu']
-                particle['c'] = d_type['c']
-                particle['fixed'] = d_type['fixed']
-        return {'particles': particles}
+                ids.append(particle['particle_id'])
+        return {'particles': ids}
 
     def convert_to_model(self):
         '''

From 72555125eb7f700e7f204c579d13e7f351269dfc Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 13:33:51 -0400
Subject: [PATCH 066/110] Fixed width of the geometry input field.

---
 client/domain-view/templates/editType.pug | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 9c2232ced2..5a01b3e256 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -103,7 +103,9 @@ div.mx-1
 
           h6.inline.mr-3 <b>Geometry</b>:
 
-          div.inline(id="type-geometry" data-hook="type-geometry")
+          div.inline(style="width: 80%")
+
+            div(id="type-geometry" data-hook="type-geometry")
 
         div.col-sm-2
 

From 97d919e6d86dab5f73b8d20e714b185a52aa063c Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 13:42:05 -0400
Subject: [PATCH 067/110] Added call to the domain views apply geometry
 function.

---
 client/domain-view/views/type-view.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 0120c1ecc4..73539d7f06 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -69,7 +69,7 @@ module.exports = View.extend({
     let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
     app.postXHR(endpoint, data, {
       success: (err, response, body) => {
-        console.log(body);
+        this.parent.parent.applyGeometry(body.particles, this.model);
       },
       error: (err, response, body) => {
         console.log(body);

From 8419a9290615b7ac77c575e6883126a5ab5aca94 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 13:50:35 -0400
Subject: [PATCH 068/110] Added a function to apply particle updates for the
 new geometry.

---
 client/domain-view/domain-view.js | 42 +++++++++++++++++++++++++++++--
 1 file changed, 40 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index 9c8a1c8d67..0145bd590c 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -150,6 +150,42 @@ module.exports = View.extend({
       this.renderImportMeshView();
     }
   },
+  applyGeometry: function (ids, type) {
+    let actPart = JSON.parse(JSON.stringify(this.actPart));
+    ids.forEach((id) => {
+      let particle = this.model.particles.get(id, 'particle_id');
+      // Set active particle for updating particle in the plot
+      this.actPart = {
+        part: particle,
+        tn: particle.type,
+        pn: this.plot.data[particle.type].ids.indexOf(particle.particle_id)
+      }
+      // Update the particle attributes
+      particle.type = type.typeID;
+      particle.mass = type.mass;
+      particle.volume = type.volume;
+      particle.rho = type.rho;
+      particle.nu = type.nu;
+      particle.c = type.c;
+      particle.fixed = type.fixed;
+      // Update the particle in the figure
+      this.changeParticleType(type.typeID, {update: false});
+    });
+    if(actPart.part) {
+      this.actPart = {
+        part: this.model.particles.get(actPart.part.particle_id, "particle_id"),
+        tn: type.typeID,
+        pn: this.plot.data[type.typeID].ids.indexOf(actPart.part.particle_id)
+      }
+      if(ids.includes(actPart.part.particle_id)) {
+        this.renderEditParticleView();
+      }
+    }else{
+      this.actPart = actPart
+    }
+    this.renderTypesView();
+    this.resetFigure();
+  },
   changeCollapseButtonText: function (e) {
     app.changeCollapseButtonText(this, e)
   },
@@ -490,13 +526,15 @@ module.exports = View.extend({
         particle.type = 0;
       }
     });
-    if(actPart.part && actPart.part.type === type) {
+    if(actPart.part) {
       this.actPart = {
         part: this.model.particles.get(actPart.part.particle_id, "particle_id"),
         tn: 0,
         pn: this.plot.data[0].ids.indexOf(actPart.part.particle_id)
       }
-      this.renderEditParticleView();
+      if(actPart.part.type === type) {
+        this.renderEditParticleView();
+      }
     }else{
       this.actPart = actPart
     }

From 8b1bcc9ceff36bd712d44f01eb6a85ac8811d0b1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 14:30:47 -0400
Subject: [PATCH 069/110] Added geometry to the type view.

---
 client/domain-view/templates/viewType.pug | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/client/domain-view/templates/viewType.pug b/client/domain-view/templates/viewType.pug
index a5953f40cb..5a0277bf4a 100644
--- a/client/domain-view/templates/viewType.pug
+++ b/client/domain-view/templates/viewType.pug
@@ -5,13 +5,23 @@ div.mx-1
 
   div.row
 
-    div.col-sm-3
+    div.col-sm-6
+
+      div.row
+
+        div.col-sm-6
+
+          div=this.model.name
+
+        div.col-sm-6
+
+          div=this.model.numParticles
 
-      div=this.model.name
+      hr
 
-    div.col-sm-3
+      h6.inline.mr-2 <b>Geometry</b>:
 
-      div=this.model.numParticles
+      div.inline=this.model.geometry
 
     div.col-sm-6
 
@@ -35,4 +45,4 @@ div.mx-1
 
             span.mr-3(for="view-td-fixed") Fixed:
 
-            input(type="checkbox" data-hook="view-td-fixed" disabled)
\ No newline at end of file
+            input(type="checkbox" data-hook="view-td-fixed" disabled)

From 69f76c1a4ec7dd4949f017302ae059ea2cb7da82 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 14:33:38 -0400
Subject: [PATCH 070/110] Added error UI for type geometry api requests.

---
 client/domain-view/templates/editType.pug | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 5a01b3e256..9dc31060ce 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -110,3 +110,7 @@ div.mx-1
         div.col-sm-2
 
           button.btn.btn-outline-secondary.box-shadow(data-hook="apply-geometry") Apply
+
+      div.mdl-edit-btn.save-error-status(data-hook="tg-error" + this.model.typeID)
+
+        span(data-hook="tg-action-error" + this.model.typeID)

From 6b5a278ff7097b0a78f9aa47b5251b6bbe79cad0 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 14:52:01 -0400
Subject: [PATCH 071/110] Added full progress UI messages.

---
 client/domain-view/templates/editType.pug | 12 +++++++++++-
 client/domain-view/views/type-view.js     | 21 ++++++++++++++++++++-
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 9dc31060ce..15f830aafd 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -111,6 +111,16 @@ div.mx-1
 
           button.btn.btn-outline-secondary.box-shadow(data-hook="apply-geometry") Apply
 
-      div.mdl-edit-btn.save-error-status(data-hook="tg-error" + this.model.typeID)
+      div.mdl-edit-btn.saving-status.inline(data-hook="tg-in-progress-" + this.model.typeID)
+
+        div.spinner-grow.mr-2
+
+        span Applying type to particles ...
+
+      div.mdl-edit-btn.saved-status.inline(data-hook="tg-complete-" + this.model.typeID)
+
+        span Type successfully applied
+
+      div.mdl-edit-btn.save-error-status(data-hook="tg-error-" + this.model.typeID)
 
         span(data-hook="tg-action-error" + this.model.typeID)
diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 73539d7f06..66b2fb0456 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -63,16 +63,30 @@ module.exports = View.extend({
     $(this.queryByHook('view-td-fixed')).prop('checked', this.model.fixed)
     app.documentSetup();
   },
+  completeAction: function () {
+    $(this.queryByHook(`tg-in-progress-${this.model.typeID}`)).css("display", "none");
+    $(this.queryByHook(`tg-complete-${this.model.typeID}`)).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook(`tg-complete-${this.model.typeID}`)).css("display", "none");
+    }, 5000);
+  },
+  errorAction: function (action) {
+    $(this.queryByHook(`tg-in-progress-${this.model.typeID}`)).css("display", "none");
+    $(this.queryByHook(`tg-action-error-${this.model.typeID}`)).text(action);
+    $(this.queryByHook(`tg-error-${this.model.typeID}`)).css("display", "block");
+  },
   handleApplyGeometry: function (e) {
+    this.startAction();
     let particles = this.model.collection.parent.particles.toJSON();
     let data = {particles: particles, type: this.model.toJSON()}
     let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
     app.postXHR(endpoint, data, {
       success: (err, response, body) => {
         this.parent.parent.applyGeometry(body.particles, this.model);
+        this.completeAction();
       },
       error: (err, response, body) => {
-        console.log(body);
+        this.errorAction(body.Message);
       }
     });
   },
@@ -106,6 +120,11 @@ module.exports = View.extend({
     this.model.fixed = e.target.checked;
     this.updateView();
   },
+  startAction: function () {
+    $(this.queryByHook(`tg-complete-${this.model.typeID}`)).css("display", "none");
+    $(this.queryByHook(`tg-error-${this.model.typeID}`)).css("display", "none");
+    $(this.queryByHook(`tg-in-progress-${this.model.typeID}`)).css("display", "inline-block");
+  },
   update: function () {},
   updateValid: function () {},
   updateView: function () {

From 021c069c79a1df20c72723e3221ff57e6ae356ee Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 15:13:12 -0400
Subject: [PATCH 072/110] Added error catch for syntax errors.

---
 stochss/handlers/util/stochss_errors.py       | 21 +++++++++++++++++++
 .../handlers/util/stochss_spatial_model.py    | 12 +++++++----
 2 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/stochss/handlers/util/stochss_errors.py b/stochss/handlers/util/stochss_errors.py
index 5599630ad8..cd2c1fb36c 100644
--- a/stochss/handlers/util/stochss_errors.py
+++ b/stochss/handlers/util/stochss_errors.py
@@ -227,6 +227,27 @@ def __init__(self, msg, trace=None):
         '''
         super().__init__(406, "Domain File Not In Proper Format", msg, trace)
 
+
+class DomainGeometryError(StochSSAPIError):
+    '''
+    ################################################################################################
+    Domain Geometry Action Failed
+    ################################################################################################
+    '''
+
+    def __init__(self, msg, trace=None):
+        '''
+        Indicates that a geometry action for the a domain failed
+
+        Attributes
+        ----------
+        msg : str
+            Details on what caused the error
+        trace : str
+            Error traceback for the error
+        '''
+        super().__init__(406, "Domain Geometry Action Failed", msg, trace)
+
 ####################################################################################################
 # Job Errors
 ####################################################################################################
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index c9f14b6dae..64972e9998 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -408,10 +408,14 @@ def inside(point):
             namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
             return eval(d_type['geometry'], {}, namespace)
         ids = []
-        for particle in particles:
-            if inside(particle['point']):
-                ids.append(particle['particle_id'])
-        return {'particles': ids}
+        try:
+            for particle in particles:
+                if inside(particle['point']):
+                    ids.append(particle['particle_id'])
+            return {'particles': ids}
+        except SyntaxError as err:
+            message = f"Failed to apply geometry. Reason given: {err}"
+            raise DomainGeometryError(message, traceback.format_exc()) from err
 
     def convert_to_model(self):
         '''

From ffd0fef1f99a5b81521def9197886d099cf48133 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 20 Jul 2022 15:29:49 -0400
Subject: [PATCH 073/110] Fixed import error.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 64972e9998..7b08575dae 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -32,7 +32,7 @@
 
 from .stochss_base import StochSSBase
 from .stochss_errors import StochSSFileNotFoundError, FileNotJSONFormatError, DomainFormatError, \
-                            StochSSModelFormatError, StochSSPermissionsError
+                            StochSSModelFormatError, StochSSPermissionsError, DomainGeometryError
 
 class StochSSSpatialModel(StochSSBase):
     '''

From 00c2f4c7ca47d6fc16d2f8618553b4f41037a850 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 08:44:13 -0400
Subject: [PATCH 074/110] Fixed typo in data hook.

---
 client/domain-view/templates/editType.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 15f830aafd..0e7feeaf56 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -123,4 +123,4 @@ div.mx-1
 
       div.mdl-edit-btn.save-error-status(data-hook="tg-error-" + this.model.typeID)
 
-        span(data-hook="tg-action-error" + this.model.typeID)
+        span(data-hook="tg-action-error-" + this.model.typeID)

From dbe30a062085268409da413a5c9da1469d41bdbf Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 08:55:05 -0400
Subject: [PATCH 075/110] Added undefined variable catch for apply geometry.

---
 stochss/handlers/util/stochss_spatial_model.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 7b08575dae..25c5e4b8ad 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -416,6 +416,9 @@ def inside(point):
         except SyntaxError as err:
             message = f"Failed to apply geometry. Reason given: {err}"
             raise DomainGeometryError(message, traceback.format_exc()) from err
+        except NameError as err:
+            message = f"Failed to apply geometry. Reason given: {err}"
+            raise DomainGeometryError(message, traceback.format_exc()) from err
 
     def convert_to_model(self):
         '''

From ba1a850bc6f636271d521d071cc67f332316f23e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 08:57:35 -0400
Subject: [PATCH 076/110] Added error processing to front end.

---
 client/domain-view/views/type-view.js | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 66b2fb0456..1fe90bfa7f 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -72,7 +72,7 @@ module.exports = View.extend({
   },
   errorAction: function (action) {
     $(this.queryByHook(`tg-in-progress-${this.model.typeID}`)).css("display", "none");
-    $(this.queryByHook(`tg-action-error-${this.model.typeID}`)).text(action);
+    $(this.queryByHook(`tg-action-error-${this.model.typeID}`)).html(action);
     $(this.queryByHook(`tg-error-${this.model.typeID}`)).css("display", "block");
   },
   handleApplyGeometry: function (e) {
@@ -86,7 +86,15 @@ module.exports = View.extend({
         this.completeAction();
       },
       error: (err, response, body) => {
-        this.errorAction(body.Message);
+        if(body.Traceback.includes("SyntaxError")) {
+          var tracePart = body.Traceback.split('\n').slice(6)
+          tracePart.splice(2, 2)
+          tracePart[1] = tracePart[1].replace(new RegExp('          ', 'g'), '                 ')
+          var errorBlock = `<p class='mb-1' style='white-space:pre'>${body.Message}<br>${tracePart.join('<br>')}</p>`
+        }else{
+          var errorBlock = body.Message
+        }
+        this.errorAction(errorBlock);
       }
     });
   },

From c6309bd02ff19400a79f40e54964d7ed1137d48d Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 09:23:15 -0400
Subject: [PATCH 077/110] Added tooltip and placeholder for geometry.

---
 client/domain-view/templates/editType.pug | 4 +++-
 client/domain-view/views/type-view.js     | 5 ++++-
 client/tooltips.js                        | 4 ++++
 3 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/templates/editType.pug b/client/domain-view/templates/editType.pug
index 0e7feeaf56..0c630182e8 100644
--- a/client/domain-view/templates/editType.pug
+++ b/client/domain-view/templates/editType.pug
@@ -101,7 +101,9 @@ div.mx-1
 
         div.col-sm-10.align-items-baseline
 
-          h6.inline.mr-3 <b>Geometry</b>:
+          h6.inline <b>Geometry</b>:
+
+          div.tooltip-icon.mr-3(data-html="true" data-toggle="tooltip" title=this.tooltips.geometry) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
           div.inline(style="width: 80%")
 
diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 1fe90bfa7f..050bfd6a01 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -21,6 +21,7 @@ let path = require('path');
 let _ = require('underscore');
 //support files
 let app = require('../../app');
+let Tooltips = require('../../tooltips');
 let tests = require('../../views/tests');
 //views
 let View = require('ampersand-view');
@@ -51,6 +52,7 @@ module.exports = View.extend({
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
     this.viewMode = attrs.viewMode ? attrs.viewMode : false;
+    this.tooltips = Tooltips.domainType;
   },
   render: function (attrs, options) {
     this.template = this.viewMode ? viewTemplate : editTemplate;
@@ -231,7 +233,8 @@ module.exports = View.extend({
           name: 'geometry',
           modelKey: 'geometry',
           valueType: 'string',
-          value: this.model.geometry
+          value: this.model.geometry,
+          placeholder: "--Expression in terms of 'x', 'y', 'z'--"
         });
       }
     }
diff --git a/client/tooltips.js b/client/tooltips.js
index f813076494..c326ec8d50 100644
--- a/client/tooltips.js
+++ b/client/tooltips.js
@@ -178,6 +178,10 @@ module.exports = {
 
     speed: "Approximate or artificial speed of sound"
   },
+  domainType: {
+    geometry: "The geometry expression can be any mathematical expression which evaluates to a boolean value in a python environment (i.e. x==5).  This "+
+        "expression is evaluable within the a limited namespace, and only lower case variables (x, y, z) can be referenced in the expression."
+  },
   boundaryConditionsEditor: {
     annotation: "An optional note about a boundary condition."
   }

From 3bda8039bc2b9842a3de42840728abaa3f10cd56 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 12:05:23 -0400
Subject: [PATCH 078/110] Fixed typo in data hook for edit limits tab content.

---
 client/domain-view/templates/limitsView.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/domain-view/templates/limitsView.pug b/client/domain-view/templates/limitsView.pug
index 6c13b2af23..3fb1868a60 100644
--- a/client/domain-view/templates/limitsView.pug
+++ b/client/domain-view/templates/limitsView.pug
@@ -22,7 +22,7 @@ div#domain-limits-editor.card
 
     div.card-body.tab-content
 
-      div.tab-pane.active(id="edit-domain-limits" data-hook="edit-domnain-limits")
+      div.tab-pane.active(id="edit-domain-limits" data-hook="edit-domain-limits")
 
         div.mx-1.row.head.align-items-baseline
 

From 205ab7ce8c6926b55fb2b67523d29c10d128291e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 12:09:36 -0400
Subject: [PATCH 079/110] Added a build function for custom geometry classes. 
 Added function to fill a geometry with particles.

---
 .../handlers/util/stochss_spatial_model.py    | 58 ++++++++++++++++++-
 1 file changed, 57 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 25c5e4b8ad..f08b9bbdbd 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -28,7 +28,8 @@
 import plotly
 from escapism import escape
 from spatialpy import Model, Species, Parameter, Reaction, Domain, DomainError, BoundaryCondition, \
-                      PlaceInitialCondition, UniformInitialCondition, ScatterInitialCondition
+                      PlaceInitialCondition, UniformInitialCondition, ScatterInitialCondition, \
+                      Geometry
 
 from .stochss_base import StochSSBase
 from .stochss_errors import StochSSFileNotFoundError, FileNotJSONFormatError, DomainFormatError, \
@@ -90,6 +91,25 @@ def expression(self): # pylint: disable=no-self-use
         return NewBC()
 
 
+    @classmethod
+    def __build_geometry(cls, d_type):
+        name = d_type['name'].title()
+        class NewG(Geometry): # pylint: disable=too-few-public-methods
+            '''
+            ########################################################################################
+            Custom SpatialPy Geometry
+            ########################################################################################
+            '''
+            __class__ = f"__main__.{name}"
+            def inside(self, point, on_boundary): # pylint: disable=no-self-use
+                '''
+                Custom inside for geometry
+                '''
+                namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
+                return eval(d_type['geometry'], {}, namespace)
+        return NewG()
+
+
     @classmethod
     def __build_stochss_domain(cls, s_domain, data=None):
         particles = cls.__build_stochss_domain_particles(s_domain=s_domain, data=data)
@@ -483,6 +503,42 @@ def create_boundary_condition(self, kwargs):
         return {"expression": expression}
 
 
+    @classmethod
+    def fill_geometry(cls, kwargs, d_type):
+        '''
+        Create particles of the given type with the given properties within the geometry.
+
+        Attributes
+        ----------
+        kwargs : dict
+            Arguments passed to Domain.fill_with_particles.
+        d_type : dict
+            StochSS type definition.
+        '''
+        kwargs['geometry_ivar'] = cls.__build_geometry(d_type)
+        kwargs['type_id'] = d_type['type_id']
+        kwargs['mass'] = d_type['mass']
+        kwargs['volume'] = d_type['volume']
+        kwargs['rho'] = d_type['rho']
+        kwargs['nu'] = d_type['nu']
+        kwargs['c'] = d_type['c']
+        kwargs['fixed'] = d_type['fixed']
+        try:
+            domain = Domain(
+                0, (kwargs['xmin'],kwargs['xmax']),
+                (kwargs['ymin'],kwargs['ymax']), (kwargs['zmin'],kwargs['zmax'])
+            )
+            domain.fill_with_particles(**kwargs)
+            particles = cls.__build_stochss_domain_particles(domain)
+            return {'particles': particles}
+        except SyntaxError as err:
+            message = f"Failed to fill geometry. Reason given: {err}"
+            raise DomainGeometryError(message, traceback.format_exc()) from err
+        except NameError as err:
+            message = f"Failed to fill geometry. Reason given: {err}"
+            raise DomainGeometryError(message, traceback.format_exc()) from err
+
+
     def get_domain(self, path=None, new=False):
         '''
         Get a prospective domain

From a54dfa90f9a2e36f4ca4d62fe37b3892d6b73314 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 21 Jul 2022 12:11:27 -0400
Subject: [PATCH 080/110] Added api handler and route for fill geometry.

---
 stochss/handlers/__init__.py |  1 +
 stochss/handlers/models.py   | 28 ++++++++++++++++++++++++++++
 2 files changed, 29 insertions(+)

diff --git a/stochss/handlers/__init__.py b/stochss/handlers/__init__.py
index 2d1ac08be9..a5df0d851b 100644
--- a/stochss/handlers/__init__.py
+++ b/stochss/handlers/__init__.py
@@ -87,6 +87,7 @@ def get_page_handlers(route_start):
         (r"/stochss/api/spatial-model/import-mesh\/?", ImportMeshAPIHandler),
         (r"/stochss/api/spatial-model/3d-domain\/?", Create3DDomainAPIHandler),
         (r"/stochss/api/spatial-model/apply-geometry\/?", ApplyGeometryAPIHandler),
+        (r"/stochss/api/spatial-model/fill-geometry\/?", FillGeometryAPIHandler),
         (r"/stochss/api/project/new-project\/?", NewProjectAPIHandler),
         (r"/stochss/api/project/load-project\/?", LoadProjectAPIHandler),
         (r"/stochss/api/project/load-browser\/?", LoadProjectBrowserAPIHandler),
diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 7105e23df7..a890ea8c41 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -510,3 +510,31 @@ async def post(self):
         except StochSSAPIError as err:
             report_error(self, log, err)
         self.finish()
+
+class FillGeometryAPIHandler(APIHandler):
+    '''
+    ################################################################################################
+    Handler fill geometry with particles.
+    ################################################################################################
+    '''
+    @web.authenticated
+    async def post(self):
+        '''
+        Fill a geomatry with particles.
+
+        Attributes
+        ----------
+        '''
+        self.set_header('Content-Type', 'application/json')
+        data = json.loads(self.request.body.decode())
+        log.debug(f"Agrs passed to Domain.fill_with_particles: {data['kwargs']}")
+        log.debug(f"Type used to fill geometry: {data['type']}")
+        try:
+            log.info("Creating particles within the geometry.")
+            resp = StochSSSpatialModel.fill_geometry(data['kwargs'], data['type'])
+            log.info("Successfully filled the geometry particles.")
+            log.debug(f"Response Message: {resp}")
+            self.write(resp)
+        except StochSSAPIError as err:
+            report_error(self, log, err)
+        self.finish()

From d461583634df818d3169dad977d0b46d43e08084 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 13:12:32 -0400
Subject: [PATCH 081/110] Created the new fill geometry particle view.

---
 .../templates/fillGeometryView.pug            | 167 +++++++++++++
 .../domain-view/views/fill-geometry-view.js   | 228 ++++++++++++++++++
 2 files changed, 395 insertions(+)
 create mode 100644 client/domain-view/templates/fillGeometryView.pug
 create mode 100644 client/domain-view/views/fill-geometry-view.js

diff --git a/client/domain-view/templates/fillGeometryView.pug b/client/domain-view/templates/fillGeometryView.pug
new file mode 100644
index 0000000000..aef662bf30
--- /dev/null
+++ b/client/domain-view/templates/fillGeometryView.pug
@@ -0,0 +1,167 @@
+div.mx-1
+
+  div
+
+    h4.inline.mr-2 Type:
+
+    div.inline(data-hook="fill-geometry-type-select")
+
+  div
+
+    h4.inline.mr-2 Geometry:
+
+    div.inline(data-hook="fill-geometry-type-geometry")
+
+  div.mt-3
+
+    h5 Type Defaults
+
+    hr
+
+    div.mb-3.mx-1.row.head.align-items-baseline
+
+      div.col-sm-2
+
+        h6.inline <b>Mass</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Volume</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Density</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Viscosity</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Speed of Sound</b>
+
+      div.col-sm-2
+
+        h6.inline <b>Fixed</b>
+
+    div.row.pl-3
+
+      div.col-sm-2
+
+        div(data-hook="fill-geometry-td-mass")
+
+      div.col-sm-2
+
+        div(data-hook="fill-geometry-td-vol")
+
+      div.col-sm-2
+
+        div(data-hook="fill-geometry-td-rho")
+
+      div.col-sm-2
+
+        div(data-hook="fill-geometry-td-nu")
+
+      div.col-sm-2
+
+        div(data-hook="fill-geometry-td-c")
+
+      div.col-sm-2
+
+        input(type="checkbox" data-hook="fill-geometry-td-fixed" disabled)
+
+  h4.mt-3 Domain Limits
+
+  div
+
+    div.mx-1.row.head.align-items-baseline
+
+      div.col-sm-3
+      
+      div.col-sm-3
+
+        h6.inline <b>X-Axis</b>
+
+      div.col-sm-3
+
+        h6.inline <b>Y-Axis</b>
+
+      div.col-sm-3
+
+        h6.inline <b>Z-Axis</b>
+
+    div.mt-3.mx-1.row
+
+      div.col-sm-3
+
+        h6.inline <b>Minimum</b>
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-x-lim-min" data-target="fill-geometry-limitation" data-name="xmin")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-y-lim-min" data-target="fill-geometry-limitation" data-name="ymin")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-z-lim-min" data-target="fill-geometry-limitation" data-name="zmin")
+
+    hr
+
+    div.mx-1.row
+
+      div.col-sm-3
+
+        h6.inline <b>Maximum</b>
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-x-lim-max" data-target="fill-geometry-limitation" data-name="xmax")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-y-lim-max" data-target="fill-geometry-limitation" data-name="ymax")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-z-lim-max" data-target="fill-geometry-limitation" data-name="zmax")
+
+    hr
+
+    div.mx-1.row
+
+      div.col-sm-3
+
+        h6.inline <b>Delta</b>
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-deltax" data-target="fill-geometry-delta" data-name="deltax")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-deltay" data-target="fill-geometry-delta" data-name="deltay")
+
+      div.col-sm-3
+
+        div(data-hook="fill-geometry-deltaz" data-target="fill-geometry-delta" data-name="deltaz")
+
+  div.inline
+
+    button.btn.btn-outline-primary(data-hook="fill-geometry" disabled) Fill with Particles
+
+  div.mdl-edit-btn.saving-status.inline(data-hook="fg-in-progress")
+
+    div.spinner-grow.mr-2
+
+    span Creating particles ...
+
+  div.mdl-edit-btn.saved-status.inline(data-hook="fg-complete")
+
+    span Particles successfully created
+
+  div.mdl-edit-btn.save-error-status(data-hook="fg-error")
+
+    span(data-hook="fg-action-error")
diff --git a/client/domain-view/views/fill-geometry-view.js b/client/domain-view/views/fill-geometry-view.js
new file mode 100644
index 0000000000..46304aae7d
--- /dev/null
+++ b/client/domain-view/views/fill-geometry-view.js
@@ -0,0 +1,228 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2022 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+let $ = require('jquery');
+let path = require('path');
+//support files
+let app = require('../../app');
+let tests = require('../../views/tests');
+//views
+let View = require('ampersand-view');
+let InputView = require('../../views/input');
+let SelectView = require('ampersand-select-view');
+//templates
+let template = require('../templates/fillGeometryView.pug');
+
+module.exports = View.extend({
+  template: template,
+  events: {
+    'change [data-hook=fill-geometry-type-select]' : 'handleTypeUpdate',
+    'change [data-target=fill-geometry-limitation]' : 'handleDataUpdate',
+    'change [data-target=fill-geometry-delta]' : 'handleDataUpdate'
+  },
+  initialize: function (attrs, options) {
+    View.prototype.initialize.apply(this, arguments);
+    this.data = {
+      "xmin":0, "ymin":0, "zmin":0, "xmax":0, "ymax":0,
+      "zmax":0, "deltax": 0, "deltay": 0, "deltaz": 0
+    }
+    this.type = null;
+  },
+  render: function (attrs, options) {
+    View.prototype.render.apply(this, arguments);
+    this.getTypes();
+    this.renderTypeSelectView();
+  },
+  disable: function () {
+    if(this.data.xmin === this.data.xmax) { return true; }
+    if(this.data.ymin === this.data.ymax) { return true; }
+    if(this.data.zmin === this.data.zmax) { return true; }
+    if(this.data.deltax === 0) { return true; }
+    if(this.data.deltay === 0) { return true; }
+    if(this.data.deltaz === 0) { return true; }
+    if(!this.type) { return true; }
+    return false;
+  },
+  getTypes: function () {
+    this.types = this.parent.model.types.filter((type) => {
+      return Boolean(type.geometry);
+    });
+    console.log(this.types)
+  },
+  handleDataUpdate: function (e) {
+    let key = e.target.parentElement.parentElement.dataset.name;
+    this.data[key] = Number(e.target.value);
+    this.toggleFillGeometry();
+  },
+  handleTypeUpdate: function (e) {
+    if(e.target.value) {
+      let typeID = Number(e.target.value);
+      this.type = this.parent.model.types.get(typeID, "typeID");
+    }else{
+      this.type = null;
+    }
+    this.updateTypeDefaults();
+    this.toggleFillGeometry();
+  },
+  renderTypeSelectView: function () {
+    if(this.typeSelectView) {
+      this.typeSelectView.remove();
+    }
+    if(this.types) {
+      var options = this.types.map((type) => {
+        return [type.typeID, type.name];
+      });
+    }else{
+      var options = [];
+    }
+    this.typeSelectView = new SelectView({
+      name: 'type',
+      required: false,
+      idAttribute: 'typeID',
+      textAttribute: 'name',
+      eagerValidate: true,
+      options: options,
+      unselectedText: "Select a Type"
+    });
+    app.registerRenderSubview(this, this.typeSelectView, "fill-geometry-type-select");
+  },
+  toggleFillGeometry: function () {
+    $(this.queryByHook('fill-geometry')).prop('disabled', this.disable());
+  },
+  update: function() {},
+  updateTypeDefaults: function () {
+    $(this.queryByHook("fill-geometry-type-geometry")).text(this.type.geometry || "");
+    $(this.queryByHook("fill-geometry-td-mass")).text(this.type.mass || "");
+    $(this.queryByHook("fill-geometry-td-vol")).text(this.type.volume || "");
+    $(this.queryByHook("fill-geometry-td-rho")).text(this.type.rho || "");
+    $(this.queryByHook("fill-geometry-td-nu")).text(this.type.nu || "0");
+    $(this.queryByHook("fill-geometry-td-c")).text(this.type.c || "");
+    $(this.queryByHook("fill-geometry-td-fixed")).prop('checked', this.type.fixed || false);
+  },
+  updateValid: function () {},
+  subviews: {
+    xMinLimInputView: {
+      hook: "fill-geometry-x-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-lim-min',
+          valueType: 'number',
+          value: this.data.xmin
+        });
+      }
+    },
+    yMinLimInputView: {
+      hook: "fill-geometry-y-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-lim-min',
+          valueType: 'number',
+          value: this.data.ymin
+        });
+      }
+    },
+    zMinLimInputView: {
+      hook: "fill-geometry-z-lim-min",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-lim-min',
+          valueType: 'number',
+          value: this.data.zmin
+        });
+      }
+    },
+    xMaxLimInputView: {
+      hook: "fill-geometry-x-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'x-lim-max',
+          valueType: 'number',
+          value: this.data.xmax
+        });
+      }
+    },
+    yMaxLimInputView: {
+      hook: "fill-geometry-y-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'y-lim-max',
+          valueType: 'number',
+          value: this.data.ymax
+        });
+      }
+    },
+    zMaxLimInputView: {
+      hook: "fill-geometry-z-lim-max",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'z-lim-max',
+          valueType: 'number',
+          value: this.data.zmax
+        });
+      }
+    },
+    deltaxInputView: {
+      hook: "fill-geometry-deltax",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'deltax',
+          valueType: 'number',
+          value: this.data.deltax
+        });
+      }
+    },
+    deltayInputView: {
+      hook: "fill-geometry-deltay",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'deltay',
+          valueType: 'number',
+          value: this.data.deltay
+        });
+      }
+    },
+    deltazInputView: {
+      hook: "fill-geometry-deltaz",
+      prepareView: function (el) {
+        return new InputView({
+          parent: this,
+          required: true,
+          name: 'deltaz',
+          valueType: 'number',
+          value: this.data.deltaz
+        });
+      }
+    },
+  }
+});
\ No newline at end of file

From 9f99cdeb625f809e8d2f1f8240581a7fd59c85df Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 13:16:06 -0400
Subject: [PATCH 082/110] Added the fill geometry view to the particles
 section.

---
 client/domain-view/domain-view.js     | 46 +++++++++++++--------------
 client/domain-view/domainView.pug     |  8 +++++
 client/domain-view/views/type-view.js |  2 ++
 3 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index 0145bd590c..cdf45f44d7 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -32,6 +32,7 @@ let QuickviewType = require('./views/quickview-type');
 let PropertiesView = require('./views/properties-view');
 let EditParticleView = require('./views/particle-view');
 let ViewParticleView = require('./views/view-particle');
+let FillGeometryView = require('./views/fill-geometry-view');
 let ImportMeshView = require('./views/import-mesh-view');
 let Edit3DDomainView = require('./views/edit-3D-domain-view');
 let TypesDescriptionView = require('./views/types-description-view');
@@ -67,11 +68,8 @@ module.exports = View.extend({
       $(this.queryByHook('domain-figure-preview')).css('display', 'none');
       this.renderTypesQuickview();
     }else{
-      this.renderNewParticleView();
-      this.renderEditParticleView();
+      this.updateParticleViews({includeGeometry: true});
       this.renderTypesDescriptionView();
-      this.renderEdit3DDomainView();
-      this.renderImportMeshView();
     }
     if(!this.elements) {
       this.elements = {
@@ -118,10 +116,7 @@ module.exports = View.extend({
     }
     this.renderTypesView();
     if(types) {
-      this.renderNewParticleView();
-      this.renderEditParticleView();
-      this.renderEdit3DDomainView();
-      this.renderImportMeshView();
+      this.updateParticleViews();
     }
     this.resetFigure();
   },
@@ -144,10 +139,7 @@ module.exports = View.extend({
     newTrace.name = name;
     this.plot.data.push(newTrace);
     if(update) {
-      this.renderNewParticleView();
-      this.renderEditParticleView();
-      this.renderEdit3DDomainView();
-      this.renderImportMeshView();
+      this.updateParticleViews();
     }
   },
   applyGeometry: function (ids, type) {
@@ -287,10 +279,7 @@ module.exports = View.extend({
     this.model.realignTypes(type);
     this.plot.data.splice(type, 1);
     this.renderTypesView();
-    this.renderNewParticleView();
-    this.renderEditParticleView();
-    this.renderEdit3DDomainView();
-    this.renderImportMeshView();
+    this.updateParticleViews({includeGeometry: true});
     this.resetFigure();
   },
   displayFigure: function () {
@@ -345,10 +334,6 @@ module.exports = View.extend({
   },
   renameType: function (index, name) {
     this.plot.data[index].name = name;
-    this.renderNewParticleView();
-    this.renderEditParticleView();
-    this.renderEdit3DDomainView();
-    this.renderImportMeshView();
     this.resetFigure();
   },
   renderEdit3DDomainView: function () {
@@ -374,6 +359,13 @@ module.exports = View.extend({
     $(this.queryByHook("save-selected-particle")).prop('disabled', disable);
     $(this.queryByHook("remove-selected-particle")).prop('disabled', disable);
   },
+  renderFillGeometryView: function () {
+    if(this.fillGeometryView) {
+      this.fillGeometryView.remove();
+    }
+    this.fillGeometryView = new FillGeometryView();
+    app.registerRenderSubview(this, this.fillGeometryView, 'fill-geometry-container');
+  },
   renderImportMeshView: function () {
     if(this.importMeshView) {
       this.importMeshView.remove();
@@ -504,10 +496,7 @@ module.exports = View.extend({
       this.actPart = actPart
     }
     this.resetFigure();
-    this.renderNewParticleView();
-    this.renderEditParticleView();
-    this.renderEdit3DDomainView();
-    this.renderImportMeshView();
+    this.updateParticleViews();
   },
   startAction: function (prefix) {
     $(this.queryByHook(`${prefix}-complete`)).css('display', 'none');
@@ -542,5 +531,14 @@ module.exports = View.extend({
       this.renderTypesView();
       this.resetFigure();
     }
+  },
+  updateParticleViews: function ({includeGeometry=false}={}) {
+    this.renderNewParticleView();
+    this.renderEditParticleView();
+    this.renderEdit3DDomainView();
+    this.renderImportMeshView();
+    if(includeGeometry) {
+      this.renderFillGeometryView();
+    }
   }
 });
diff --git a/client/domain-view/domainView.pug b/client/domain-view/domainView.pug
index cf03c36301..5e47982687 100644
--- a/client/domain-view/domainView.pug
+++ b/client/domain-view/domainView.pug
@@ -36,6 +36,10 @@ div#domain-view
 
             a.nav-link.tab(data-hook="import-particles-tab" data-toggle="tab" href="#import-particles") Import Mesh
 
+          li.nav-item
+
+            a.nav-link.tab(data-hook="fill-geometry-tab" data-toggle="tab" href="#fill-geometry") Fill Geometry
+
       button.btn.btn-outline-collapse(data-toggle="collapse" data-target="#domain-particles-section" data-hook="collapse-domain-particles") -
 
     div.collapse.show(id="domain-particles-section" data-hook="domain-particles-section")
@@ -101,6 +105,10 @@ div#domain-view
 
           div(data-hook="import-particles-container")
 
+        div.tab-pane(id="fill-geometry" data-hook="fill-geometry-section")
+
+          div(data-hook="fill-geometry-container")
+
   div#domain-figure-preview.card(data-hook="domain-figure-preview")
 
     div.card-header.pb-0
diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 050bfd6a01..022b67f895 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -43,6 +43,7 @@ module.exports = View.extend({
     'change [data-hook=type-name]' : 'handleRenameType',
     'change [data-target=type-defaults]' : 'updateView',
     'change [data-hook=td-fixed]' : 'setTDFixed',
+    'change [data-hook=type-geometry]' : 'updateView',
     'click [data-hook=select]' : 'selectType',
     'click [data-hook=unassign-all]' : 'handleUnassignParticles',
     'click [data-hook=delete-type]' : 'handleDeleteType',
@@ -139,6 +140,7 @@ module.exports = View.extend({
   updateValid: function () {},
   updateView: function () {
     this.parent.renderViewTypeView();
+    this.parent.parent.updateParticleViews({includeGeometry: true});
   },
   subviews: {
     inputTypeID: {

From 1f5561c2f40dc5f8bbe9449dfa000357ad950f3d Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 13:40:50 -0400
Subject: [PATCH 083/110] Added support of center coords.

---
 stochss/handlers/models.py                    |  2 +-
 .../handlers/util/stochss_spatial_model.py    | 26 ++++++++++++++-----
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index a890ea8c41..d6c8fa61c6 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -503,7 +503,7 @@ async def post(self):
         log.debug(f"Type used to apply geometry: {data['type']}")
         try:
             log.info("Applying type and properties to particles.")
-            resp = StochSSSpatialModel.apply_geometry(data['particles'], data['type'])
+            resp = StochSSSpatialModel.apply_geometry(data['particles'], data['type'], data['center'])
             log.info("Successfully applied type and properties to particles.")
             log.debug(f"Response Message: {resp}")
             self.write(resp)
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index f08b9bbdbd..dd8cd7d2cd 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -92,7 +92,7 @@ def expression(self): # pylint: disable=no-self-use
 
 
     @classmethod
-    def __build_geometry(cls, d_type):
+    def __build_geometry(cls, d_type, center):
         name = d_type['name'].title()
         class NewG(Geometry): # pylint: disable=too-few-public-methods
             '''
@@ -101,13 +101,19 @@ class NewG(Geometry): # pylint: disable=too-few-public-methods
             ########################################################################################
             '''
             __class__ = f"__main__.{name}"
+            def __init__(self, center):
+                self.center = center
+
             def inside(self, point, on_boundary): # pylint: disable=no-self-use
                 '''
                 Custom inside for geometry
                 '''
-                namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
+                namespace = {
+                    'cx': self.center[0], 'cy': self.center[1], 'cz': self.center[2],
+                    'x': point[0], 'y': point[1], 'z': point[2]
+                }
                 return eval(d_type['geometry'], {}, namespace)
-        return NewG()
+        return NewG(center)
 
 
     @classmethod
@@ -423,9 +429,12 @@ def __update_domain(self, domain=None):
 
 
     @classmethod
-    def apply_geometry(cls, particles, d_type):
+    def apply_geometry(cls, particles, d_type, center):
         def inside(point):
-            namespace = {'x': point[0], 'y': point[1], 'z': point[2]}
+            namespace = {
+                'cx': center[0], 'cy': center[1], 'cz': center[2],
+                'x': point[0], 'y': point[1], 'z': point[2]
+            }
             return eval(d_type['geometry'], {}, namespace)
         ids = []
         try:
@@ -515,7 +524,12 @@ def fill_geometry(cls, kwargs, d_type):
         d_type : dict
             StochSS type definition.
         '''
-        kwargs['geometry_ivar'] = cls.__build_geometry(d_type)
+        center = [
+            kwargs['xmax'] - kwargs['xmin'],
+            kwargs['ymax'] - kwargs['ymin'],
+            kwargs['zmax'] - kwargs['zmin']
+        ]
+        kwargs['geometry_ivar'] = cls.__build_geometry(d_type, center)
         kwargs['type_id'] = d_type['type_id']
         kwargs['mass'] = d_type['mass']
         kwargs['volume'] = d_type['volume']

From 8d8ca6040e0f58f8d900fd0be23e3fb6d63626d0 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 13:45:18 -0400
Subject: [PATCH 084/110] Updated tooltip to include geometry center.

---
 client/tooltips.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/client/tooltips.js b/client/tooltips.js
index c326ec8d50..067224de3f 100644
--- a/client/tooltips.js
+++ b/client/tooltips.js
@@ -180,7 +180,8 @@ module.exports = {
   },
   domainType: {
     geometry: "The geometry expression can be any mathematical expression which evaluates to a boolean value in a python environment (i.e. x==5).  This "+
-        "expression is evaluable within the a limited namespace, and only lower case variables (x, y, z) can be referenced in the expression."
+        "expression is evaluable within the a limited namespace, and only lower case variables (x, y, z), particles location, and (cx, cy, cz), "+
+        "center of the geometry, can be referenced in the expression."
   },
   boundaryConditionsEditor: {
     annotation: "An optional note about a boundary condition."

From 46fda856870ae5a893cc271a51b5082532828232 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 14:23:52 -0400
Subject: [PATCH 085/110] Added center to apply geometry.

---
 client/domain-view/views/type-view.js | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 022b67f895..f83ddc2a80 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -80,8 +80,14 @@ module.exports = View.extend({
   },
   handleApplyGeometry: function (e) {
     this.startAction();
-    let particles = this.model.collection.parent.particles.toJSON();
-    let data = {particles: particles, type: this.model.toJSON()}
+    let domain = this.model.collection.parent;
+    let particles = domain.particles.toJSON();
+    let center = [
+      domain.x_lim[1] - domain.x_lim[0],
+      domain.y_lim[1] - domain.y_lim[0],
+      domain.z_lim[1] - domain.z_lim[0]
+    ];
+    let data = {particles: particles, type: this.model.toJSON(), center: center}
     let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
     app.postXHR(endpoint, data, {
       success: (err, response, body) => {

From 9d27608cb88e0ef2ff9bfb26f8d781f6e1a8e4b2 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 14:31:10 -0400
Subject: [PATCH 086/110] Added limits to response.

---
 stochss/handlers/util/stochss_spatial_model.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index dd8cd7d2cd..4d920cc51f 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -544,7 +544,8 @@ def fill_geometry(cls, kwargs, d_type):
             )
             domain.fill_with_particles(**kwargs)
             particles = cls.__build_stochss_domain_particles(domain)
-            return {'particles': particles}
+            limits = {'x_lim': domain.xlim, 'y_lim': domain.ylim, 'z_lim': domain.zlim}
+            return {'particles': particles, 'limits': limits}
         except SyntaxError as err:
             message = f"Failed to fill geometry. Reason given: {err}"
             raise DomainGeometryError(message, traceback.format_exc()) from err

From 3a3661704a702e42b3e15c204c5722a02685da62 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 14:34:46 -0400
Subject: [PATCH 087/110] Added handler for fill geometry.

---
 .../domain-view/views/fill-geometry-view.js   | 40 ++++++++++++++++++-
 1 file changed, 39 insertions(+), 1 deletion(-)

diff --git a/client/domain-view/views/fill-geometry-view.js b/client/domain-view/views/fill-geometry-view.js
index 46304aae7d..4d5e8b6e35 100644
--- a/client/domain-view/views/fill-geometry-view.js
+++ b/client/domain-view/views/fill-geometry-view.js
@@ -48,6 +48,13 @@ module.exports = View.extend({
     this.getTypes();
     this.renderTypeSelectView();
   },
+  completeAction: function () {
+    $(this.queryByHook("fg-in-progress")).css("display", "none");
+    $(this.queryByHook("fg-complete")).css("display", "inline-block");
+    setTimeout(() => {
+      $(this.queryByHook("fg-complete")).css("display", "none");
+    }, 5000);
+  },
   disable: function () {
     if(this.data.xmin === this.data.xmax) { return true; }
     if(this.data.ymin === this.data.ymax) { return true; }
@@ -58,17 +65,43 @@ module.exports = View.extend({
     if(!this.type) { return true; }
     return false;
   },
+  errorAction: function (action) {
+    $(this.queryByHook("fg-in-progress")).css("display", "none");
+    $(this.queryByHook("fg-action-error")).html(action);
+    $(this.queryByHook("fg-error")).css("display", "block");
+  },
   getTypes: function () {
     this.types = this.parent.model.types.filter((type) => {
       return Boolean(type.geometry);
     });
-    console.log(this.types)
   },
   handleDataUpdate: function (e) {
     let key = e.target.parentElement.parentElement.dataset.name;
     this.data[key] = Number(e.target.value);
     this.toggleFillGeometry();
   },
+  handleFillGeometry: function () {
+    this.startAction();
+    let data = {kwargs: this.data, type: this.type}
+    let endpoint = path.join(app.getApiPath(), 'spatial-model/fill-geometry');
+    app.postXHR(endpoint, data, {
+      success: (err, response, body) => {
+        this.parent.parent.add3DDomain(body.limits, body.particles);
+        this.completeAction();
+      },
+      error: (err, response, body) => {
+        if(body.Traceback.includes("SyntaxError")) {
+          var tracePart = body.Traceback.split('\n').slice(6)
+          tracePart.splice(2, 2)
+          tracePart[1] = tracePart[1].replace(new RegExp('          ', 'g'), '                 ')
+          var errorBlock = `<p class='mb-1' style='white-space:pre'>${body.Message}<br>${tracePart.join('<br>')}</p>`
+        }else{
+          var errorBlock = body.Message
+        }
+        this.errorAction(errorBlock);
+      }
+    });
+  },
   handleTypeUpdate: function (e) {
     if(e.target.value) {
       let typeID = Number(e.target.value);
@@ -101,6 +134,11 @@ module.exports = View.extend({
     });
     app.registerRenderSubview(this, this.typeSelectView, "fill-geometry-type-select");
   },
+  startAction: function () {
+    $(this.queryByHook("fg-complete")).css("display", "none");
+    $(this.queryByHook("fg-error")).css("display", "none");
+    $(this.queryByHook("fg-in-progress")).css("display", "inline-block");
+  },
   toggleFillGeometry: function () {
     $(this.queryByHook('fill-geometry')).prop('disabled', this.disable());
   },

From 732e30b6d0a1d43839227ddc8af51736be12b838 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 14:45:01 -0400
Subject: [PATCH 088/110] Added missing event handler.  Fixed name error.

---
 client/domain-view/views/fill-geometry-view.js | 3 ++-
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/views/fill-geometry-view.js b/client/domain-view/views/fill-geometry-view.js
index 4d5e8b6e35..ff83c09c31 100644
--- a/client/domain-view/views/fill-geometry-view.js
+++ b/client/domain-view/views/fill-geometry-view.js
@@ -33,7 +33,8 @@ module.exports = View.extend({
   events: {
     'change [data-hook=fill-geometry-type-select]' : 'handleTypeUpdate',
     'change [data-target=fill-geometry-limitation]' : 'handleDataUpdate',
-    'change [data-target=fill-geometry-delta]' : 'handleDataUpdate'
+    'change [data-target=fill-geometry-delta]' : 'handleDataUpdate',
+    'click [data-hook=fill-geometry]' : 'handleFillGeometry'
   },
   initialize: function (attrs, options) {
     View.prototype.initialize.apply(this, arguments);
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 4d920cc51f..ac6dca03da 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -530,7 +530,7 @@ def fill_geometry(cls, kwargs, d_type):
             kwargs['zmax'] - kwargs['zmin']
         ]
         kwargs['geometry_ivar'] = cls.__build_geometry(d_type, center)
-        kwargs['type_id'] = d_type['type_id']
+        kwargs['type_id'] = d_type['typeID']
         kwargs['mass'] = d_type['mass']
         kwargs['volume'] = d_type['volume']
         kwargs['rho'] = d_type['rho']

From 4e0a2e84299f5d69cddb8ac85f4dc473f6c264e8 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 14:53:32 -0400
Subject: [PATCH 089/110] Fixed type error.

---
 stochss/handlers/util/stochss_spatial_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index ac6dca03da..57d253aa76 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -532,7 +532,7 @@ def fill_geometry(cls, kwargs, d_type):
         kwargs['geometry_ivar'] = cls.__build_geometry(d_type, center)
         kwargs['type_id'] = d_type['typeID']
         kwargs['mass'] = d_type['mass']
-        kwargs['volume'] = d_type['volume']
+        kwargs['vol'] = d_type['volume']
         kwargs['rho'] = d_type['rho']
         kwargs['nu'] = d_type['nu']
         kwargs['c'] = d_type['c']

From 41bab25f57fd9ecc7e6c7a107a260745b99568fc Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Sun, 24 Jul 2022 15:12:06 -0400
Subject: [PATCH 090/110] Fixed response processing.

---
 client/domain-view/domain-view.js              | 2 +-
 client/domain-view/views/fill-geometry-view.js | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/domain-view/domain-view.js b/client/domain-view/domain-view.js
index cdf45f44d7..6afabcda6f 100644
--- a/client/domain-view/domain-view.js
+++ b/client/domain-view/domain-view.js
@@ -89,7 +89,7 @@ module.exports = View.extend({
     }
   },
   add3DDomain: function (limits, particles) {
-    let limitsChanged = this.changeDomainLimits(limits, Boolean(plot));
+    let limitsChanged = this.changeDomainLimits(limits, false);
     particles.forEach((particle) => {
       particle = new Particle(particle);
       this.model.particles.addParticle({particle: particle});
diff --git a/client/domain-view/views/fill-geometry-view.js b/client/domain-view/views/fill-geometry-view.js
index ff83c09c31..f9f507f3a9 100644
--- a/client/domain-view/views/fill-geometry-view.js
+++ b/client/domain-view/views/fill-geometry-view.js
@@ -87,7 +87,7 @@ module.exports = View.extend({
     let endpoint = path.join(app.getApiPath(), 'spatial-model/fill-geometry');
     app.postXHR(endpoint, data, {
       success: (err, response, body) => {
-        this.parent.parent.add3DDomain(body.limits, body.particles);
+        this.parent.add3DDomain(body.limits, body.particles);
         this.completeAction();
       },
       error: (err, response, body) => {

From 17d4b4cffd7eb1590340b26f696db78a4e908ff1 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Jul 2022 13:00:28 -0400
Subject: [PATCH 091/110] Fixed center calculations.

---
 client/domain-view/views/type-view.js          |  6 +++---
 stochss/handlers/util/stochss_spatial_model.py | 10 +++++++---
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index f83ddc2a80..0c3bcb2cc4 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -83,9 +83,9 @@ module.exports = View.extend({
     let domain = this.model.collection.parent;
     let particles = domain.particles.toJSON();
     let center = [
-      domain.x_lim[1] - domain.x_lim[0],
-      domain.y_lim[1] - domain.y_lim[0],
-      domain.z_lim[1] - domain.z_lim[0]
+      (domain.x_lim[1] + domain.x_lim[0]) / 2,
+      (domain.y_lim[1] + domain.y_lim[0]) / 2,
+      (domain.z_lim[1] + domain.z_lim[0]) / 2
     ];
     let data = {particles: particles, type: this.model.toJSON(), center: center}
     let endpoint = path.join(app.getApiPath(), 'spatial-model/apply-geometry');
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 57d253aa76..03a8982452 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -525,11 +525,13 @@ def fill_geometry(cls, kwargs, d_type):
             StochSS type definition.
         '''
         center = [
-            kwargs['xmax'] - kwargs['xmin'],
-            kwargs['ymax'] - kwargs['ymin'],
-            kwargs['zmax'] - kwargs['zmin']
+            (kwargs['xmax'] + kwargs['xmin']) / 2,
+            (kwargs['ymax'] + kwargs['ymin']) / 2,
+            (kwargs['zmax'] + kwargs['zmin']) / 2
         ]
         kwargs['geometry_ivar'] = cls.__build_geometry(d_type, center)
+        print(kwargs['geometry_ivar'].center)
+        print(kwargs['geometry_ivar'].inside([0, 0, 0], False))
         kwargs['type_id'] = d_type['typeID']
         kwargs['mass'] = d_type['mass']
         kwargs['vol'] = d_type['volume']
@@ -537,12 +539,14 @@ def fill_geometry(cls, kwargs, d_type):
         kwargs['nu'] = d_type['nu']
         kwargs['c'] = d_type['c']
         kwargs['fixed'] = d_type['fixed']
+        print(kwargs)
         try:
             domain = Domain(
                 0, (kwargs['xmin'],kwargs['xmax']),
                 (kwargs['ymin'],kwargs['ymax']), (kwargs['zmin'],kwargs['zmax'])
             )
             domain.fill_with_particles(**kwargs)
+            print(len(domain.vertices))
             particles = cls.__build_stochss_domain_particles(domain)
             limits = {'x_lim': domain.xlim, 'y_lim': domain.ylim, 'z_lim': domain.zlim}
             return {'particles': particles, 'limits': limits}

From dc531a9d5d1174fe1779fd8ee053bfeca6d8fa0d Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 26 Jul 2022 13:33:53 -0400
Subject: [PATCH 092/110] Fixed type assignment for new particles.

---
 stochss/handlers/util/stochss_spatial_model.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 03a8982452..1aa4d30fee 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -153,7 +153,7 @@ def __build_stochss_domain_particles(cls, s_domain, data=None):
             else:
                 viscosity = data['type']['nu']
                 fixed = data['type']['fixed']
-                type_id = data['typeID']
+                type_id = data['typeID'] if 'typeID' in data.keys() else data['type']['typeID']
             point = list(vertex)
             if data is not None and data['transformation'] is not None:
                 point = [coord + data['transformation'][i] for i, coord in enumerate(point)]
@@ -530,24 +530,21 @@ def fill_geometry(cls, kwargs, d_type):
             (kwargs['zmax'] + kwargs['zmin']) / 2
         ]
         kwargs['geometry_ivar'] = cls.__build_geometry(d_type, center)
-        print(kwargs['geometry_ivar'].center)
-        print(kwargs['geometry_ivar'].inside([0, 0, 0], False))
-        kwargs['type_id'] = d_type['typeID']
+        kwargs['type_id'] = d_type['name']
         kwargs['mass'] = d_type['mass']
         kwargs['vol'] = d_type['volume']
         kwargs['rho'] = d_type['rho']
         kwargs['nu'] = d_type['nu']
         kwargs['c'] = d_type['c']
         kwargs['fixed'] = d_type['fixed']
-        print(kwargs)
         try:
             domain = Domain(
                 0, (kwargs['xmin'],kwargs['xmax']),
                 (kwargs['ymin'],kwargs['ymax']), (kwargs['zmin'],kwargs['zmax'])
             )
             domain.fill_with_particles(**kwargs)
-            print(len(domain.vertices))
-            particles = cls.__build_stochss_domain_particles(domain)
+            data = {'type': d_type, 'transformation': None}
+            particles = cls.__build_stochss_domain_particles(domain, data=data)
             limits = {'x_lim': domain.xlim, 'y_lim': domain.ylim, 'z_lim': domain.zlim}
             return {'particles': particles, 'limits': limits}
         except SyntaxError as err:

From 30f1203dedec8757a2fdcec273d23724a77c506c Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Tue, 9 Aug 2022 16:16:08 -0400
Subject: [PATCH 093/110] Updated the GillesPy2 version to v1.7.0

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 9ea7f6ee31..2a7f978088 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,6 +2,6 @@ python-libsbml==5.18.0
 python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
-gillespy2==1.6.10
+gillespy2==1.7.0
 spatialpy==1.0.4
 git+https://github.com/StochSS/sciope.git@master

From 2dc024b4af8dd4d7046b81c48a0ebe045ec5075b Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Wed, 10 Aug 2022 15:58:10 -0400
Subject: [PATCH 094/110] Excluded hidden directories for type description
 files.

---
 stochss/handlers/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/models.py b/stochss/handlers/models.py
index 4072f163af..be126a253d 100644
--- a/stochss/handlers/models.py
+++ b/stochss/handlers/models.py
@@ -349,7 +349,7 @@ async def get(self):
         try:
             folder = StochSSFolder(path="")
             test = lambda ext, root, file: bool(
-                "trash" in root.split("/") or file.startswith('.') or 'wkfl' in root
+                "trash" in root.split("/") or file.startswith('.') or 'wkfl' in root or root.startswith('.')
             )
             resp = folder.get_file_list(ext=".txt", test=test)
             log.debug("Response: {resp}")

From bff0eac10f70b4dc10ec6979331ae996d0ca1245 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Wed, 10 Aug 2022 16:01:50 -0400
Subject: [PATCH 095/110] Removed spaces from 3D Cylinder domain example.

---
 public_models/3D_Cylinder/3D_cylinder.domn | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public_models/3D_Cylinder/3D_cylinder.domn b/public_models/3D_Cylinder/3D_cylinder.domn
index dab1a00bbc..702ffe3a51 100644
--- a/public_models/3D_Cylinder/3D_cylinder.domn
+++ b/public_models/3D_Cylinder/3D_cylinder.domn
@@ -1 +1 @@
-{"size": null, "rho_0": 1.0, "c_0": 10, "p_0": 10, "gravity": [0, 0, 0], "x_lim": [-5.0, 5.0], "y_lim": [-1.0, 0.9999999999999999], "z_lim": [-0.9997191433003008, 0.9999488265847117], "boundary_condition": {"reflect_x": true, "reflect_y": true, "reflect_z": true}, "particles": [{"particle_id": 1, "point": [-2.101682616989703, -0.964452787824742, 0.2489313344981683], "volume": 0.015135255135374578, "mass": 0.015135255135374578, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 2, "point": [-1.887513465434122, -0.5014916255865332, 0.06961314329212905], "volume": 0.07034111605740352, "mass": 0.07034111605740352, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 3, "point": [-1.757042722631912, -0.9228641348563182, 0.3845831077631754], "volume": 0.02382667425447659, "mass": 0.02382667425447659, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 4, "point": [-1.85413888369328, -0.9955594999585697, 0.04508515352682077], "volume": 0.01837175522796916, "mass": 0.01837175522796916, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 5, "point": [1.874975500982107, 0.2492223157132696, -0.2524856754824046], "volume": 0.04863919527628578, "mass": 0.04863919527628578, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 6, "point": [1.808320438516406, 0.05711590686461099, -0.6164182499126918], "volume": 0.0632175288192508, "mass": 0.0632175288192508, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 7, "point": [2.182529343210714, -0.1663114027612958, -0.4557993633541657], "volume": 0.05566341760973872, "mass": 0.05566341760973872, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 8, "point": [2.06222242502517, -0.06584170406028653, -0.09390309609504216], "volume": 0.05094615682555442, "mass": 0.05094615682555442, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 9, "point": [-2.380044639472586, 0.1039603942187995, -0.6660021716554381], "volume": 0.027613011065781377, "mass": 0.027613011065781377, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 10, "point": [-2.305676947241498, -0.3113331410231057, -0.589095101307394], "volume": 0.043631235211839, "mass": 0.043631235211839, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 11, "point": [-2.262942990799641, -0.04111516086018868, -0.9959505101076245], "volume": 0.02307565554258796, "mass": 0.02307565554258796, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 12, "point": [-2.093631369619373, -0.04820563757950643, -0.6060599358098253], "volume": 0.053285055209458865, "mass": 0.053285055209458865, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 13, "point": [-1.999792859336622, -0.94943344706238, -0.2984434655811745], "volume": 0.013863453851301994, "mass": 0.013863453851301994, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 14, "point": [-1.754728853599724, -0.8801338975074484, -0.464525759047439], "volume": 0.006452758616580852, "mass": 0.006452758616580852, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 15, "point": [-1.689826608177531, -0.5981799589653591, -0.2304829208262158], "volume": 0.06319118564277616, "mass": 0.06319118564277616, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 16, "point": [-1.670428874777768, -0.9736314258341583, -0.2186734200213536], "volume": 0.012063450996053436, "mass": 0.012063450996053436, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 17, "point": [3.590501737794977, -0.4310110060573188, -0.3131780598352483], "volume": 0.06390075032081181, "mass": 0.06390075032081181, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 18, "point": [3.257879943487412, -0.4243756833306612, 0.07732536880979513], "volume": 0.03900782913147994, "mass": 0.03900782913147994, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 19, "point": [3.160881489131067, -0.4731490872585901, -0.3414347939235592], "volume": 0.07191513330511291, "mass": 0.07191513330511291, "type": 1, "nu": 0.0, "fixed": false}, {"particle_id": 20, "point": [3.4964304507652, 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From 891bb3589bfa0e1cfa54eb900535d26ad47eeaf5 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Wed, 10 Aug 2022 16:04:59 -0400
Subject: [PATCH 096/110] Removed spaces from domain types in 3D Cylinder
 example model.

---
 public_models/3D_Cylinder/3D_cylinder.smdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public_models/3D_Cylinder/3D_cylinder.smdl b/public_models/3D_Cylinder/3D_cylinder.smdl
index 87f03f038a..740aa54412 100644
--- a/public_models/3D_Cylinder/3D_cylinder.smdl
+++ b/public_models/3D_Cylinder/3D_cylinder.smdl
@@ -1 +1 @@
-{"annotation":"SpatialPy 3D Cylinder Demo Model","defaultID":9,"defaultMode":"discrete","domain":{"boundary_condition":{"reflect_x":true,"reflect_y":true,"reflect_z":true},"c_0":10,"gravity":[0, 0, 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\\emptyset","types":[1,2,3]}],"rules":[],"species":[{"annotation":"","compID":1,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"A","switchMin":100,"switchTol":0.03,"types":[1,2],"value":0,"diffusionConst":0.1},{"annotation":"","compID":2,"diffusionCoeff":0.1,"isSwitchTol":true,"mode":"discrete","name":"B","switchMin":100,"switchTol":0.03,"types":[1,3],"value":0,"diffusionConst":0.1}],"volume":1,"name":"cylinder_demo3d"}

From 4a9440eb262bf9dce6a1455041229acf639ab7fe Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Aug 2022 18:14:11 -0400
Subject: [PATCH 097/110] Updated set particles types tab name.

---
 client/domain-view/domainView.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/domain-view/domainView.pug b/client/domain-view/domainView.pug
index 5e47982687..646a80baa5 100644
--- a/client/domain-view/domainView.pug
+++ b/client/domain-view/domainView.pug
@@ -26,7 +26,7 @@ div#domain-view
 
           li.nav-item
 
-            a.nav-link.tab(data-hook="particle-types-tab" data-toggle="tab" href="#set-particle-types") Set Particle Types
+            a.nav-link.tab(data-hook="particle-types-tab" data-toggle="tab" href="#set-particle-types") Set Types from File
 
           li.nav-item
 

From bb0d2e07eaedc7cc6ca4abc696ae8bd371036acc Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Aug 2022 18:14:42 -0400
Subject: [PATCH 098/110] Changes deltas to spacing.

---
 client/domain-view/templates/fillGeometryView.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/domain-view/templates/fillGeometryView.pug b/client/domain-view/templates/fillGeometryView.pug
index aef662bf30..e9f2400326 100644
--- a/client/domain-view/templates/fillGeometryView.pug
+++ b/client/domain-view/templates/fillGeometryView.pug
@@ -134,7 +134,7 @@ div.mx-1
 
       div.col-sm-3
 
-        h6.inline <b>Delta</b>
+        h6.inline <b>Spacing</b>
 
       div.col-sm-3
 

From 437bb555ac14d1e98a2c5d57757898e80b5bf780 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Wed, 10 Aug 2022 18:15:55 -0400
Subject: [PATCH 099/110] Fixed issue with initial condition creation in
 notebooks .

---
 stochss/handlers/util/stochss_notebook.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index e96ba80ed8..6cd905a67d 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -297,7 +297,7 @@ def __create_model_cell(self):
             model.extend([f"    {type_id.upper()} = '{type_id}'" for type_id in type_ids.values()])
             model.extend(["", "    def __init__(self):",
                           f'{pad}Model.__init__(self, name="{self.get_name()}")'])
-            type_refs = {index: type_id.upper() for index, type_id in type_ids.items()}
+            type_refs = {index: type_id for index, type_id in type_ids.items()}
             self.__create_domain_string(model=model, pad=pad)
             self.__create_boundary_condition_string(model=model, pad=pad)
             self.__create_species_strings(model=model, pad=pad, type_refs=type_refs)

From 4c1572f3173a46b15f372ed7864a9e9b33ddfca9 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 11 Aug 2022 13:19:19 -0400
Subject: [PATCH 100/110] Added error catch for fill geometry that catches
 spatialpy model errors.

---
 stochss/handlers/util/stochss_spatial_model.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 4a1559920c..f03afddee6 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -29,7 +29,7 @@
 from escapism import escape
 from spatialpy import Model, Species, Parameter, Reaction, Domain, DomainError, BoundaryCondition, \
                       PlaceInitialCondition, UniformInitialCondition, ScatterInitialCondition, \
-                      Geometry
+                      Geometry, ModelError
 
 from .stochss_base import StochSSBase
 from .stochss_errors import StochSSFileNotFoundError, FileNotJSONFormatError, DomainFormatError, \
@@ -555,6 +555,9 @@ def fill_geometry(cls, kwargs, d_type):
         except NameError as err:
             message = f"Failed to fill geometry. Reason given: {err}"
             raise DomainGeometryError(message, traceback.format_exc()) from err
+        except ModelError as err:
+            message = f"Failed to fill geometry. Reason given: {err}"
+            raise DomainGeometryError(message, traceback.format_exc()) from err
 
 
     def get_domain(self, path=None, new=False):

From 47bc5e01b05336e616f86d0291433025adf1d99f Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 11 Aug 2022 14:12:57 -0400
Subject: [PATCH 101/110] Added test to type_id input view to inform users of
 invalid chars.

---
 client/domain-view/views/type-view.js |  1 +
 client/views/tests.js                 | 73 +++++++++++++++------------
 2 files changed, 41 insertions(+), 33 deletions(-)

diff --git a/client/domain-view/views/type-view.js b/client/domain-view/views/type-view.js
index 0c3bcb2cc4..ea2ac60f3d 100644
--- a/client/domain-view/views/type-view.js
+++ b/client/domain-view/views/type-view.js
@@ -157,6 +157,7 @@ module.exports = View.extend({
           required: true,
           name: 'name',
           modelKey: 'name',
+          tests: [tests.invalidChar],
           valueType: 'string',
           value: this.model.name
         });
diff --git a/client/views/tests.js b/client/views/tests.js
index f60be1c432..7773d5c350 100644
--- a/client/views/tests.js
+++ b/client/views/tests.js
@@ -16,38 +16,45 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
 
+let startChar = (text) => {
+  if (/^[0-9]+/.test(text)) {
+    return "Field cannot start with a number. Start with letter or underscore." 
+  }
+}
+
+let invalidChar = (text) => {
+  if (!/^[a-zA-Z0-9_]+$/.test(text)) {
+    return "Invalid characters. Please only use letters, numbers, or underscores."
+  }
+}
+
+let nanValue = (value) => {
+  if (isNaN(Number(value))) {
+    return "Must be a number."
+  }
+}
+
+let negValue = (value) => {
+  if (Number(value) < 0) {
+    return "Must be non-negative."
+  }
+}
+
+// function (text) {
+//   if(this.parent.model && this.parent.model.collection){
+//     var isDuplicate = this.parent.model.collection.some(function (m) { return m.name === text && this.parent.model !== m;
+//     }, this);
+//     if (isDuplicate) {
+//       return "No duplicate entries."
+//     }
+//   }
+// },
+
 module.exports = {
-  nameTests: [
-    function (text) {
-      if (/^[0-9]+/.test(text)) {
-        return "Field cannot start with a number. Start with letter or underscore." 
-      }
-    },
-    function (text) {
-      if (!/^[a-zA-Z0-9_]+$/.test(text)) {
-        return "Invalid characters. Please only use letters, numbers, or underscores."
-      }
-    },
-    // function (text) {
-    //   if(this.parent.model && this.parent.model.collection){
-    //     var isDuplicate = this.parent.model.collection.some(function (m) { return m.name === text && this.parent.model !== m;
-    //     }, this);
-    //     if (isDuplicate) {
-    //       return "No duplicate entries."
-    //     }
-    //   }
-    // },
-  ],
-  valueTests: [
-    function (value) {
-      if (isNaN(Number(value))) {
-        return "Must be a number."
-      }
-    },
-    function (value) {
-      if (Number(value) < 0) {
-        return "Must be non-negative."
-      }
-    },
-  ],
+  invalidChar: invalidChar,
+  nameTests: [startChar, invalidChar],
+  nanValue: nanValue,
+  negValue: negValue,
+  startChar: startChar,
+  valueTests: [nanValue, negValue]
 }
\ No newline at end of file

From 9c9af2e7c81aec6665c71fa76057ceb32613ffd9 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Thu, 11 Aug 2022 14:14:02 -0400
Subject: [PATCH 102/110] Fixed issue with empty view tab in domain section of
 model editor.

---
 client/model-view/templates/domainViewer.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/model-view/templates/domainViewer.pug b/client/model-view/templates/domainViewer.pug
index 830b30a5b9..d675aa0174 100644
--- a/client/model-view/templates/domainViewer.pug
+++ b/client/model-view/templates/domainViewer.pug
@@ -41,7 +41,7 @@ div#domain-viewer.card
 
             div.inline(data-hook="select-location")
 
-        div(data-hook="domain-view-container")
+      div(data-hook="domain-view-container")
 
       div.tab-pane.active(id="edit-domain" data-hook="edit-domain")
 

From 755cfe03bb5815c839dcc69357bbe208acf4c459 Mon Sep 17 00:00:00 2001
From: BryanRumsey <44621966+BryanRumsey@users.noreply.github.com>
Date: Mon, 15 Aug 2022 09:04:45 -0400
Subject: [PATCH 103/110] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 2a7f978088..c8a3d64a92 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,5 +3,5 @@ python-libsedml==2.0.9
 python-libcombine==0.2.7
 escapism==1.0.1
 gillespy2==1.7.0
-spatialpy==1.0.4
+spatialpy==1.1.0
 git+https://github.com/StochSS/sciope.git@master

From bcd3f0efe814d839126b8dc7343cbcaf41506131 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 15 Aug 2022 13:29:51 -0400
Subject: [PATCH 104/110] Fixed typo in the spatial mode labels.

---
 client/model-view/modelView.pug | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/model-view/modelView.pug b/client/model-view/modelView.pug
index def5cf4d6c..8fea01cd20 100644
--- a/client/model-view/modelView.pug
+++ b/client/model-view/modelView.pug
@@ -49,7 +49,7 @@ div#model-view
               span Concentration
             div.col-sm-4
               input.mr-2(type="radio" name="default-mode" data-hook="spatial-discrete" data-name="discrete")
-              span Population (outpust: absolute value)
+              span Population (outputs: absolute value)
             div.col-sm-4
               input.mr-2(type="radio" name="default-mode" data-hook="spatial-discrete-concentration" data-name="discrete-concentration")
               span Population (outputs: scaled by volume)

From 636c7b037dc2f2ba5dc71096f975b563ae8d3e64 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 15 Aug 2022 13:30:58 -0400
Subject: [PATCH 105/110] Fixed intgration bug between stochss and spatialpy.

---
 stochss/handlers/util/stochss_spatial_model.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index eee1fe7d40..7c8ac6e038 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -618,11 +618,11 @@ def get_particles_from_3d_domain(self, data):
         dimensions += bool(ylim[1] - ylim[0])
         dimensions += bool(zlim[1] - zlim[0])
         if dimensions > 2:
-            s_domain = Domain.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, nx=data['nx'],
-                                               ny=data['ny'], nz=data['nz'], **data['type'])
+            s_domain = Domain.create_3D_domain(xlim=xlim, ylim=ylim, zlim=zlim, numx=data['nx'],
+                                               numy=data['ny'], numz=data['nz'], **data['type'])
         else:
             s_domain = Domain.create_2D_domain(xlim=xlim, ylim=ylim,
-                                               nx=data['nx'], ny=data['ny'], **data['type'])
+                                               numx=data['nx'], numy=data['ny'], **data['type'])
         domain = self.__build_stochss_domain(s_domain=s_domain, data=data)
         limits = {"x_lim":domain['x_lim'], "y_lim":domain['y_lim'], "z_lim":domain['z_lim']}
         resp = {"particles":domain['particles'], "limits":limits}

From 232be9f9ab77b025cb7c7573592e36e594c2bc7c Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 15 Aug 2022 13:31:36 -0400
Subject: [PATCH 106/110] Fixed key error in notebook gen.

---
 stochss/handlers/util/stochss_notebook.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/stochss/handlers/util/stochss_notebook.py b/stochss/handlers/util/stochss_notebook.py
index e96ba80ed8..7e5c15ff0e 100644
--- a/stochss/handlers/util/stochss_notebook.py
+++ b/stochss/handlers/util/stochss_notebook.py
@@ -349,8 +349,9 @@ def __create_reaction_strings(self, model, pad, type_refs=None):
 
                     reac_str = f'{pad}{reac["name"]} = Reaction(name="{reac["name"]}", '
                     reac_str += f'reactants={react_str}, products={prod_str}, '
-                    if reac['reactionType'] == 'custom-propensity':
+                    if not reac['massaction']:
                         reac_str += f'propensity_function="{reac["propensity"]}"'
+                        reac_str += f'odepropensity_function="{reac["odePropensity"]}"'
                     else:
                         reac_str += f'rate="{reac["rate"]["name"]}"'
                     if self.s_model['is_spatial']:

From da555b3df88e4ce131d9bb18b632d810bc49c924 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Mon, 15 Aug 2022 15:04:02 -0400
Subject: [PATCH 107/110] Implemented template versioning.

---
 client/models/domain.js                       |  3 +-
 client/models/model.js                        |  3 +-
 stochss/handlers/util/stochss_base.py         |  1 +
 .../handlers/util/stochss_spatial_model.py    | 86 ++++++++++---------
 .../nonSpatialModelTemplate.json              |  6 +-
 5 files changed, 54 insertions(+), 45 deletions(-)

diff --git a/client/models/domain.js b/client/models/domain.js
index 72ea2428fc..137e9c38f4 100644
--- a/client/models/domain.js
+++ b/client/models/domain.js
@@ -33,7 +33,8 @@ module.exports = State.extend({
     x_lim: 'object',
     y_lim: 'object',
     z_lim: 'object',
-    static: 'boolean'
+    static: 'boolean',
+    template_version: 'number'
   },
   collections: {
     types: Types,
diff --git a/client/models/model.js b/client/models/model.js
index 076612620c..c993e86c91 100644
--- a/client/models/model.js
+++ b/client/models/model.js
@@ -43,7 +43,8 @@ module.exports = Model.extend({
     defaultID: 'number',
     defaultMode: 'string',
     annotation: 'string',
-    volume: 'any'
+    volume: 'any',
+    template_version: 'number'
   },
   collections: {
     species: Species,
diff --git a/stochss/handlers/util/stochss_base.py b/stochss/handlers/util/stochss_base.py
index 4ce6b4a9bc..53e4fac822 100644
--- a/stochss/handlers/util/stochss_base.py
+++ b/stochss/handlers/util/stochss_base.py
@@ -32,6 +32,7 @@ class StochSSBase():
     ################################################################################################
     '''
     user_dir = os.path.expanduser("~") # returns the path to the users home directory
+    TEMPLATE_VERSION = 1
 
     def __init__(self, path):
         '''
diff --git a/stochss/handlers/util/stochss_spatial_model.py b/stochss/handlers/util/stochss_spatial_model.py
index 6f1be2e99f..9f45ec33dd 100644
--- a/stochss/handlers/util/stochss_spatial_model.py
+++ b/stochss/handlers/util/stochss_spatial_model.py
@@ -405,27 +405,29 @@ def __update_domain(self, domain=None):
             if "domain" not in self.model.keys() or len(self.model['domain'].keys()) < 6:
                 self.model['domain'] = self.get_model_template()['domain']
             domain = self.model['domain']
-        if "static" not in domain.keys():
-            domain['static'] = True
-        type_changes = {}
-        for i, d_type in enumerate(domain['types']):
-            if d_type['typeID'] != i:
-                type_changes[d_type['typeID']] = i
-                d_type['typeID'] = i
-            if "rho" not in d_type.keys():
-                d_type['rho'] = d_type['mass'] / d_type['volume']
-            if "c" not in d_type.keys():
-                d_type['c'] = 10
-            if "geometry" not in d_type.keys():
-                d_type['geometry'] = ""
-        if domain['particles']:
-            for particle in domain['particles']:
-                if particle['type'] in type_changes:
-                    particle['type'] = type_changes[particle['type']]
-                if "rho" not in particle.keys():
-                    particle['rho'] = particle['mass'] / particle['volume']
-                if "c" not in particle.keys():
-                    particle['c'] = 10
+        if "template_version" not in domain or domain['template_version'] != self.TEMPLATE_VERSION:
+            if "static" not in domain.keys():
+                domain['static'] = True
+            type_changes = {}
+            for i, d_type in enumerate(domain['types']):
+                if d_type['typeID'] != i:
+                    type_changes[d_type['typeID']] = i
+                    d_type['typeID'] = i
+                if "rho" not in d_type.keys():
+                    d_type['rho'] = d_type['mass'] / d_type['volume']
+                if "c" not in d_type.keys():
+                    d_type['c'] = 10
+                if "geometry" not in d_type.keys():
+                    d_type['geometry'] = ""
+            if domain['particles']:
+                for particle in domain['particles']:
+                    if particle['type'] in type_changes:
+                        particle['type'] = type_changes[particle['type']]
+                    if "rho" not in particle.keys():
+                        particle['rho'] = particle['mass'] / particle['volume']
+                    if "c" not in particle.keys():
+                        particle['c'] = 10
+            domain['template_version'] = self.TEMPLATE_VERSION
 
 
     @classmethod
@@ -779,26 +781,28 @@ def load(self):
         if self.model is None:
             self.__read_model_file()
         self.model['name'] = self.get_name()
-        if not self.model['defaultMode']:
-            self.model['defaultMode'] = "discrete"
-        elif self.model['defaultMode'] == "dynamic":
-            self.model['defaultMode'] = "discrete-concentration"
-        if "timestepSize" not in self.model['modelSettings'].keys():
-            self.model['modelSettings']['timestepSize'] = 1e-5
-        self.__update_domain()
-        if "boundaryConditions" not in self.model.keys():
-            self.model['boundaryConditions'] = []
-        for species in self.model['species']:
-            if "types" not in species.keys():
-                species['types'] = list(range(1, len(self.model['domain']['types'])))
-            if "diffusionConst" not in species.keys():
-                diff = 0.0 if "diffusionCoeff" not in species.keys() else species['diffusionCoeff']
-                species['diffusionConst'] = diff
-        for reaction in self.model['reactions']:
-            if "odePropensity" not in reaction.keys():
-                reaction['odePropensity'] = reaction['propensity']
-            if "types" not in reaction.keys():
-                reaction['types'] = list(range(1, len(self.model['domain']['types'])))
+        if "template_version" not in self.model or self.model['template_version'] != self.TEMPLATE_VERSION:
+            if not self.model['defaultMode']:
+                self.model['defaultMode'] = "discrete"
+            elif self.model['defaultMode'] == "dynamic":
+                self.model['defaultMode'] = "discrete-concentration"
+            if "timestepSize" not in self.model['modelSettings'].keys():
+                self.model['modelSettings']['timestepSize'] = 1e-5
+            self.__update_domain()
+            if "boundaryConditions" not in self.model.keys():
+                self.model['boundaryConditions'] = []
+            for species in self.model['species']:
+                if "types" not in species.keys():
+                    species['types'] = list(range(1, len(self.model['domain']['types'])))
+                if "diffusionConst" not in species.keys():
+                    diff = 0.0 if "diffusionCoeff" not in species.keys() else species['diffusionCoeff']
+                    species['diffusionConst'] = diff
+            for reaction in self.model['reactions']:
+                if "odePropensity" not in reaction.keys():
+                    reaction['odePropensity'] = reaction['propensity']
+                if "types" not in reaction.keys():
+                    reaction['types'] = list(range(1, len(self.model['domain']['types'])))
+            self.model['template_version'] = self.TEMPLATE_VERSION
         return self.model
 
 
diff --git a/stochss_templates/nonSpatialModelTemplate.json b/stochss_templates/nonSpatialModelTemplate.json
index 415672303f..d422dfd9d6 100644
--- a/stochss_templates/nonSpatialModelTemplate.json
+++ b/stochss_templates/nonSpatialModelTemplate.json
@@ -35,7 +35,8 @@
                 "volume":1.0
             }
         ],
-        "particles": []
+        "particles": [],
+        "template_version": 1
     },
 	"species": [],
     "initialConditions": [],
@@ -44,5 +45,6 @@
 	"rules": [],
 	"eventsCollection": [],
 	"functionDefinitions": [],
-	"boundaryConditions": []
+	"boundaryConditions": [],
+	"template_version": 1
 }

From ee6e3acc8fedf43b66aac9500b67cd112fb64cce Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 16 Aug 2022 13:27:53 -0400
Subject: [PATCH 108/110] Fixed file not found error.

---
 stochss/handlers/util/stochss_folder.py | 59 +++++++++++++------------
 1 file changed, 31 insertions(+), 28 deletions(-)

diff --git a/stochss/handlers/util/stochss_folder.py b/stochss/handlers/util/stochss_folder.py
index b5d29f732a..202d77dabd 100644
--- a/stochss/handlers/util/stochss_folder.py
+++ b/stochss/handlers/util/stochss_folder.py
@@ -456,36 +456,39 @@ def get_presentations(cls):
         Attributes
         ----------
         '''
-        path = os.path.join(cls.user_dir, ".presentations")
-        files = [file for file in os.listdir(path) if not file.startswith('.')]
         presentations = []
-        if not files:
+        try:
+            path = os.path.join(cls.user_dir, ".presentations")
+            files = [file for file in os.listdir(path) if not file.startswith('.')]
+            if not files:
+                return presentations
+            names = cls.__get_names_from_file(path, files)
+            need_names = not bool(names)
+            safe_chars = set(string.ascii_letters + string.digits)
+            hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars)
+            for file in files:
+                file_path = os.path.join(path, file)
+                ctime = os.path.getctime(file_path)
+                routes = {
+                    "smdl": "present-model",
+                    "mdl": "present-model",
+                    "job": "present-job",
+                    "ipynb": "present-notebook"
+                }
+                name, ext = cls.__get_presentation_name(names, file, file_path)
+                presentation = {
+                    "file": file, "name": f"{name}.{ext}",
+                    "link": f"/stochss/{routes[ext]}?owner={hostname}&file={file}",
+                    "size": os.path.getsize(file_path),
+                    "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
+                }
+                presentations.append(presentation)
+            if need_names or len(names.keys()) != len(files):
+                with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
+                    json.dump(names, names_file)
+            return presentations
+        except FileNotFoundError:
             return presentations
-        names = cls.__get_names_from_file(path, files)
-        need_names = not bool(names)
-        safe_chars = set(string.ascii_letters + string.digits)
-        hostname = escape(os.environ.get('JUPYTERHUB_USER'), safe=safe_chars)
-        for file in files:
-            file_path = os.path.join(path, file)
-            ctime = os.path.getctime(file_path)
-            routes = {
-                "smdl": "present-model",
-                "mdl": "present-model",
-                "job": "present-job",
-                "ipynb": "present-notebook"
-            }
-            name, ext = cls.__get_presentation_name(names, file, file_path)
-            presentation = {
-                "file": file, "name": f"{name}.{ext}",
-                "link": f"/stochss/{routes[ext]}?owner={hostname}&file={file}",
-                "size": os.path.getsize(file_path),
-                "ctime": datetime.datetime.fromtimestamp(ctime).strftime("%b %d, %Y")
-            }
-            presentations.append(presentation)
-        if need_names or len(names.keys()) != len(files):
-            with open(os.path.join(path, ".presentation_names.json"), "w") as names_file:
-                json.dump(names, names_file)
-        return presentations
 
 
     def get_project_list(self):

From fe538aacb909250feff2483b99c06b071c51dc6e Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 16 Aug 2022 13:30:52 -0400
Subject: [PATCH 109/110] Removed navigation when saving domains to file.

---
 client/pages/domain-editor.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/pages/domain-editor.js b/client/pages/domain-editor.js
index 530612da2a..9a489a61e9 100644
--- a/client/pages/domain-editor.js
+++ b/client/pages/domain-editor.js
@@ -126,7 +126,6 @@ let DomainEditor = PageView.extend({
       this.model.saveModel(() => {
         this.completeAction("Domain saved to model");
       });
-      window.location.replace(this.getBreadcrumbData().model.href);
     }
   },
   handleSaveToFile: function () {

From ff9404d11cdc7b4affa84176ea13feda829be4d7 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 16 Aug 2022 14:26:09 -0400
Subject: [PATCH 110/110] Added handlers for network errors.

---
 client/app.js | 54 ++++++++++++++++++++++++++++++++-------------------
 1 file changed, 34 insertions(+), 20 deletions(-)

diff --git a/client/app.js b/client/app.js
index af22f9612a..786121e86f 100644
--- a/client/app.js
+++ b/client/app.js
@@ -100,31 +100,45 @@ let registerRenderSubview = (parent, view, hook) => {
 let getXHR = (endpoint, {
   always = function (err, response, body) {}, success = function (err, response, body) {},
   error = function (err, response, body) {}}={}) => {
-  xhr({uri: endpoint, json: true}, function (err, response, body) {
-    if(response.statusCode < 400) {
-      success(err, response, body);
-    }else if(response.statusCode < 500) {
-      error(err, response, body);
-    }else{
-      console.log("Critical Error Detected");
-    }
-    always(err, response, body);
-  });
+  try {
+    xhr({uri: endpoint, json: true}, function (err, response, body) {
+      if(response.statusCode < 400) {
+        success(err, response, body);
+      }else if(response.statusCode < 500) {
+        error(err, response, body);
+      }else{
+        console.log("Critical Error Detected");
+      }
+      always(err, response, body);
+    });
+  }catch(exception){
+    console.log(exception);
+    let response = {Reason: "Network Error", Message: exception};
+    let body = {response: response, err: exception}
+    error(exception, response, body);
+  }
 };
 
 let postXHR = (endpoint, data, {
   always = function (err, response, body) {}, success = function (err, response, body) {},
   error = function (err, response, body) {}}={}, isJSON) => {
-  xhr({uri: endpoint, json: isJSON !== undefined ? isJSON : true, method: "post", body: data}, function (err, response, body) {
-    if(response.statusCode < 400) {
-      success(err, response, body);
-    }else if(response.statusCode < 500) {
-      error(err, response, body);
-    }else{
-      console.log("Critical Error Detected");
-    }
-    always(err, response, body);
-  });
+  try {
+    xhr({uri: endpoint, json: isJSON !== undefined ? isJSON : true, method: "post", body: data}, function (err, response, body) {
+      if(response.statusCode < 400) {
+        success(err, response, body);
+      }else if(response.statusCode < 500) {
+        error(err, response, body);
+      }else{
+        console.log("Critical Error Detected");
+      }
+      always(err, response, body);
+    });
+  }catch(exception){
+    console.log(exception);
+    let response = {Reason: "Network Error", Message: exception};
+    let body = {response: response, err: exception}
+    error(exception, response, body);
+  }
 };
 
 let getBrowser = () => {